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Wei, Dan, Qingshan Jiang, and Sheng Li. "A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases." International Journal of Nanotechnology and Molecular Computation 2, no. 4 (October 2010): 1–11. http://dx.doi.org/10.4018/978-1-60960-064-8.ch006.
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Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of length L, reflects the valuable information contained in a biological sequence and thus may be used in DNA sequence similarity analysis. However, similarity analysis based on characteristic distribution of L-tuple is not effective for the comparison of highly conservative sequences. In this paper, a new similarity measurement approach based on Triplets of Nucleic Acid Bases (TNAB) is introduced for DNA sequence similarity analysis. The new approach characterizes both the content feature and position feature of a DNA sequence using the frequency and position of occurrence of TNAB in the sequence. The experimental results show that the approach based on TNAB is effective for analysing DNA sequence similarity.
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Li, Hongliang, and Bin Liu. "BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo." PLOS Computational Biology 19, no. 6 (June 20, 2023): e1011214. http://dx.doi.org/10.1371/journal.pcbi.1011214.
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As the key for biological sequence structure and function prediction, disease diagnosis and treatment, biological sequence similarity analysis has attracted more and more attentions. However, the exiting computational methods failed to accurately analyse the biological sequence similarities because of the various data types (DNA, RNA, protein, disease, etc) and their low sequence similarities (remote homology). Therefore, new concepts and techniques are desired to solve this challenging problem. Biological sequences (DNA, RNA and protein sequences) can be considered as the sentences of “the book of life”, and their similarities can be considered as the biological language semantics (BLS). In this study, we are seeking the semantics analysis techniques derived from the natural language processing (NLP) to comprehensively and accurately analyse the biological sequence similarities. 27 semantics analysis methods derived from NLP were introduced to analyse biological sequence similarities, bringing new concepts and techniques to biological sequence similarity analysis. Experimental results show that these semantics analysis methods are able to facilitate the development of protein remote homology detection, circRNA-disease associations identification and protein function annotation, achieving better performance than the other state-of-the-art predictors in the related fields. Based on these semantics analysis methods, a platform called BioSeq-Diabolo has been constructed, which is named after a popular traditional sport in China. The users only need to input the embeddings of the biological sequence data. BioSeq-Diabolo will intelligently identify the task, and then accurately analyse the biological sequence similarities based on biological language semantics. BioSeq-Diabolo will integrate different biological sequence similarities in a supervised manner by using Learning to Rank (LTR), and the performance of the constructed methods will be evaluated and analysed so as to recommend the best methods for the users. The web server and stand-alone package of BioSeq-Diabolo can be accessed at http://bliulab.net/BioSeq-Diabolo/server/.
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de Oliveira Martins, Leonardo, Alison E. Mather, and Andrew J. Page. "Scalable neighbour search and alignment with uvaia." PeerJ 12 (March 6, 2024): e16890. http://dx.doi.org/10.7717/peerj.16890.
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Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.
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Van Reenen, C. A., W. H. Van Zyl, and L. M. T. Dicks. "Expression of the Immunity Protein of Plantaricin 423, Produced by Lactobacillus plantarum 423, and Analysis of the Plasmid Encoding the Bacteriocin." Applied and Environmental Microbiology 72, no. 12 (October 20, 2006): 7644–51. http://dx.doi.org/10.1128/aem.01428-06.
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ABSTRACT Plantaricin 423 is a class IIa bacteriocin produced by Lactobacillus plantarum isolated from sorghum beer. It has been previously determined that plantaricin 423 is encoded by a plasmid designated pPLA4, which is now completely sequenced. The plantaricin 423 operon shares high sequence similarity with the operons of coagulin, pediocin PA-1, and pediocin AcH, with small differences in the DNA sequence encoding the mature bacteriocin peptide and the immunity protein. Apart from the bacteriocin operon, no significant sequence similarity could be detected between the DNA or translated sequence of pPLA4 and the available DNA or translated sequences of the plasmids encoding pediocin AcH, pediocin PA-1, and coagulin, possibly indicating a different origin. In addition to the bacteriocin operon, sequence analysis of pPLA4 revealed the presence of two open reading frames (ORFs). ORF1 encodes a putative mobilization (Mob) protein that is homologous to the pMV158 superfamily of mobilization proteins. Highest sequence similarity occurred between this protein and the Mob protein of L. plantarum NCDO 1088. ORF2 encodes a putative replication protein that revealed low sequence similarity to replication proteins of plasmids pLME300 from Lactobacillus fermentum and pYIT356 from Lactobacillus casei. The immunity protein of plantaricin 423 contains 109 amino acids. Although plantaricin 423 shares high sequence similarity with the pediocin PA-1 operon, no cross-reactivity was recorded between the immunity proteins of plantaricin 423 and pediocin PA-1.
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Pacheco, Richard C., Jonas Moraes-Filho, Arlei Marcili, Leonardo J. Richtzenhain, Matias P. J. Szabó, Márcia H. B. Catroxo, Donald H. Bouyer, and Marcelo B. Labruna. "Rickettsia monteiroi sp. nov., Infecting the Tick Amblyomma incisum in Brazil." Applied and Environmental Microbiology 77, no. 15 (June 17, 2011): 5207–11. http://dx.doi.org/10.1128/aem.05166-11.
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ABSTRACTFree-living adultAmblyomma incisumticks were collected in an Atlantic rainforest area at Intervales State Park, State of São Paulo, Brazil. From anA. incisumspecimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genesgltA,htrA,rrs, andsca1on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of thegltA,htrA,rrs, andsca1genes, respectively, were sequenced. By BLAST analysis, the partial sequence ofrrsof theA. incisumrickettsial isolate was closest to the corresponding sequence ofRickettsia bellii(99.1% similarity). ThegltApartial sequence was closest to the corresponding sequences of “CandidatusRickettsia tarasevichiae” (96.1% similarity) andRickettsia canadensis(95.8% similarity). ThehtrApartial sequence was closest to the corresponding sequence ofR. canadensis(89.8% similarity). Thesca1partial sequence was closest to the corresponding sequence ofR. canadensis(95.2% similarity). Since our rickettsial isolate was genetically distinct from otherRickettsiaspecies, we propose a new species designatedRickettsia monteiroisp. nov. Phylogenetic analyses indicated thatR. monteiroibelongs to the canadensis group within the genusRickettsia, together with the speciesR. canadensisand “CandidatusR. tarasevichiae”. Little or no antibody cross-reaction was observed between sera ofR. monteiroi-inoculated guinea pigs andR. bellii-,Rickettsia rickettsii-, orR. canadensis-inoculated guinea pigs.
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Smallwood, M., J. N. Keen, and D. J. Bowles. "Purification and partial sequence analysis of plant annexins." Biochemical Journal 270, no. 1 (August 15, 1990): 157–61. http://dx.doi.org/10.1042/bj2700157.
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A fractionation procedure for annexins involving Ca2(+)-dependent binding to exogenous phospholipid was applied to tomato suspension culture cells. Two polypeptides (34 kDa and 35.5 kDa) were purified and separated from each other and from contaminant pectic polysaccharide by ion-exchange chromatography. After proteolytic digestion of SDS/PAGE-purified products, N-terminal sequencing of the peptide fragments revealed substantial similarity to sequences of known members of the annexin family characterized from a range of animal tissues. In particular, sequence similarity to the 70-amino acid-residue repeat region found in all annexins sequenced to date was present in both of the plant proteins. The data are discussed within the context of annexin involvement in Ca2(+)-mediated events in higher plants.
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Györgyey, János, Danièle Vaubert, José I. Jiménez-Zurdo, Celine Charon, Liliane Troussard, Ádám Kondorosi, and Éva Kondorosi. "Analysis of Medicago truncatula Nodule Expressed Sequence Tags." Molecular Plant-Microbe Interactions® 13, no. 1 (January 2000): 62–71. http://dx.doi.org/10.1094/mpmi.2000.13.1.62.
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Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two hundred fifty-six ESTs exhibited significant similarities to characterized data base entries and 40 of them represented 26 nodulin genes, while 133 had no similarity to sequences with known function. Only 60 out of the 389 cDNA clones corresponded to previously submitted M. truncatula EST sequences. For 117 cDNAs, reverse Northern (RNA) hybridization with root and nodule RNA probes revealed enhanced expression in the nodule, 48 clones are likely to code for novel nodulins, 33 cDNAs are clones of already known nodulin genes, and 36 clones exhibit similarity to other characterized genes. Thus, systematic analysis of the EST sequences and their expression patterns is a powerful way to identify nodule-specific and nodulation-related genes.
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Xu, Fuyu, and Kate Beard. "A Unifying Framework for Analysis of Spatial-Temporal Event Sequence Similarity and Its Applications." ISPRS International Journal of Geo-Information 10, no. 9 (September 9, 2021): 594. http://dx.doi.org/10.3390/ijgi10090594.
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Measures of similarity or differences between data objects are applied frequently in geography, biology, computer science, linguistics, logic, business analytics, and statistics, among other fields. This work focuses on event sequence similarity among event sequences extracted from time series observed at spatially deployed monitoring locations with the aim of enhancing the understanding of process similarity over time and geospatial locations. We present a framework for a novel matrix-based spatiotemporal event sequence representation that unifies punctual and interval-based representation of events. This unified representation of spatiotemporal event sequences (STES) supports different event data types and provides support for data mining and sequence classification and clustering. The similarity measure is based on the Jaccard index with temporal order constraints and accommodates different event data types. The approach is demonstrated through simulated data examples and the performance of the similarity measures is evaluated with a k-nearest neighbor algorithm (k-NN) classification test on synthetic datasets. As a case study, we demonstrate the use of these similarity measures in a spatiotemporal analysis of event sequences extracted from space time series of a water quality monitoring system.
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Nikhila, K. S., and Vrinda V. Nair. "Protein Sequence Similarity Analysis Using Computational Techniques." Materials Today: Proceedings 5, no. 1 (2018): 724–31. http://dx.doi.org/10.1016/j.matpr.2017.11.139.
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Hark Gan, Hin, Rebecca A. Perlow, Sharmili Roy, Joy Ko, Min Wu, Jing Huang, Shixiang Yan, et al. "Analysis of Protein Sequence/Structure Similarity Relationships." Biophysical Journal 83, no. 5 (November 2002): 2781–91. http://dx.doi.org/10.1016/s0006-3495(02)75287-9.
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Shah, Mohammad Monir, Hirotoshi Iihara, Makiko Noda, Sun Xiao Song, Pham Hong Nhung, Kiyofumi Ohkusu, Yoshiaki Kawamura, and Takayuki Ezaki. "dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus." International Journal of Systematic and Evolutionary Microbiology 57, no. 1 (January 1, 2007): 25–30. http://dx.doi.org/10.1099/ijs.0.64205-0.
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In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA–DNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.
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Lu, Yue, Long Zhao, Zhao Li, and Xiangjun Dong. "Genetic Similarity Analysis Based on Positive and Negative Sequence Patterns of DNA." Symmetry 12, no. 12 (December 16, 2020): 2090. http://dx.doi.org/10.3390/sym12122090.
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Similarity analysis of DNA sequences can clarify the homology between sequences and predict the structure of, and relationship between, them. At the same time, the frequent patterns of biological sequences explain not only the genetic characteristics of the organism, but they also serve as relevant markers for certain events of biological sequences. However, most of the aforementioned biological sequence similarity analysis methods are targeted at the entire sequential pattern, which ignores the missing gene fragment that may induce potential disease. The similarity analysis of such sequences containing a missing gene item is a blank. Consequently, some sequences with missing bases are ignored or not effectively analyzed. Thus, this paper presents a new method for DNA sequence similarity analysis. Using this method, we first mined not only positive sequential patterns, but also sequential patterns that were missing some of the base terms (collectively referred to as negative sequential patterns). Subsequently, we used these frequent patterns for similarity analysis on a two-dimensional plane. Several experiments were conducted in order to verify the effectiveness of this algorithm. The experimental results demonstrated that the algorithm can obtain various results through the selection of frequent sequential patterns and that accuracy and time efficiency was improved.
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Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (April 16, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.1.
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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.
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Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (September 2, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.2.
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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.
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Ai, Liang, Jie Feng, and Yu Hua Yao. "A Novel Fast Approach for Protein Classification and Evolutionary Analysis." Match Communications in Mathematical and in Computer Chemistry 90, no. 2 (April 2023): 381–98. http://dx.doi.org/10.46793/match.90-2.381a.
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In this paper, we propose a new fast alignment-free method for protein sequence similarity and evolutionary analysis. First 20 natural amino acids are clustered into 6 groups based on their physicochemical properties, then a 12-dimensional vector is constructed based on the frequency and the average position of occurrence of amino acids in each reduced amino acid sequences. Finally, the Euclidean distance is used to measure the similarity and evolutionary distance between protein sequences. The test on three datasets shows that our method can cluster each protein sequence accurately, which illustrates the effective of our method.
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Leonardo, F. C., A. F. da Cunha, M. J. da Silva, M. F. Carazzolle, A. M. Costa-Leonardo, F. F. Costa, and G. A. Pereira. "Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi." Bulletin of Entomological Research 101, no. 4 (December 21, 2010): 383–91. http://dx.doi.org/10.1017/s0007485310000556.
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AbstractThe lower termite, Coptotermes gestroi (Isoptera: Rhinotermitidae), is originally from Southeast Asia and has become a pest in Brazil. The main goal of this study was to survey C. gestroi transcriptome composition. To accomplish this, we sequenced and analyzed 3003 expressed sequence tags (ESTs) isolated from libraries of worker heads. After assembly, 695 uniESTs were obtained from which 349 have similarity with known sequences. Comparison with insect genomes demonstrated similarity, primarily with genes from Apis mellifera (28%), Tribolium castaneum (28%) and Aedes aegypti (10%). Notably, we identified two endogenous cellulases in the sequences, which may be of interest for biotechnological applications. The results presented in this work represent the first genomic study of the Asian subterranean termite, Coptotermes gestroi.
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Elzinga, Cees H., and Matthias Studer. "Normalization of Distance and Similarity in Sequence Analysis." Sociological Methods & Research 48, no. 4 (August 13, 2019): 877–904. http://dx.doi.org/10.1177/0049124119867849.
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We explore the relations between the notion of distance and a feature set–based concept of similarity and show that this concept of similarity has a spatial interpretation that is complementary to distance: it is interpreted as “direction.” Furthermore, we show how proper normalization leads to distances that can be directly interpreted as dissimilarity: Closeness in normalized space implies and is implied by similarity of the same objects, while remoteness implies and is implied by dissimilarity. Finally, we show how, in research into destandardization of the life course, properly normalizing may drastically and unequivocally change our interpretation of intercohortal distances.
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Verma, Archana, Mr R.K.Bharti, and Prof R. K. Singh. "DNA sequence comparison based on Tabular Representation." INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY 4, no. 1 (February 1, 2013): 172–75. http://dx.doi.org/10.24297/ijct.v4i1c.3121.
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DNA sequence comparison remains as one of the critical steps in the analysis of phylogenetic relationships between species. In order to get quantitative comparison, we want to devise an algorithm that would use the tabular representation of DNA sequences. The tabular approach of representation captures the essence of the base composition and distribution of the sequence. In this contribution, we take the tabular notation for DNA sequences and then these tables are compared to find the similarity/dissimilarity measure of the sequences. We have developed algorithms for comparing DNA sequences. These programs help us to search similar segments of sequences, calculate similarity scores and identify repetitions based on local sequence similarity. There are two approaches: one is to find the exact similarity and another is to find the measurement for similarity. The first approach is more sensitive, which can be used to search DNA sequence similarities only if complete matches occurred and can compare exactly similar sequences only. This approach violates if a single mismatch for any base character appears so it is not a general solution. To find the miss matches along with the matches we have suggested another approach which compiles the information matrix based on matches and miss matches. This approach is quiet general in terms of sequences which have a large fragment common with less no of dissimilar base characters. This alternate approach includes an additional step in the calculation of the similarity score that denotes multiple regions of similarity between sequences. For both these approaches computer programs are prepared and tested on data sets. These programs can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. In addition, these programs have been generalized to allow comparison of DNA sequences based on a variety of alternative scoring matrices. We have been developing tools for the analysis of protein The method is very simple and fast, and it can be used to analyze both short and long DNA sequences. The utility of this method is tested on the several sequences of species and the results are consistent with that reported.
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Wirya, Gusti Ngurah Alit Susanta, I. Wayan Diksa Gargita, and I. Putu Sudiarta. "MOLECULAR IDENTIFICATION OF FUNGI THE CAUSAL AGENT OF STRAWBERRY WILT DISEASE IN BALI." International Journal of Biosciences and Biotechnology 7, no. 2 (June 16, 2020): 64. http://dx.doi.org/10.24843/ijbb.2020.v07.i02.p02.
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The development of strawberry farming in Bali experiencing some obstacles that cause a decline in production, such as wilting disease. The disease was reported caused by the fungi base on morphological recognition. There are two fungi were recognized caused the strawberry wilt disease in Bali, they are from genus Verticillium and Fusarium. More specific information about causal agent of wilt disease in strawberry especially in Bali is needed. The one accurate identification is done through the molecular approach by analyzing DNA that encode the ribosomal DNA (rDNA). The 18S rDNA, including the internal areas of transcribed spacers (ITS), ITS1 and ITS4 have been widely used in phylogenetic studies. The amplification results of this area produce bands in different sizes that can be used to identify fungal species. Based on that the identification of strawberry wilt disease using molecular analysis was conducted. The 542 bp of Internal Transcribed Spacer (ITS) DNA was successfully amplified using PCR with pairing primers ITS 1 (5-TCCGTAGGTGAACCTGCGG-3’), and ITS 4 (5’-TCCTCCGCTTATTGATATGC-3’). The sequences of three isolates were successfully obtained through sequencing. Homology levels were tested between sequences and showed that Candi Kuning sequence and Gobleg sequence had 95% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. While Pancasari sequence have 94% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. Candi Kuning, Gobleg, and Pancasari sequences had the same 86% with sequence of Fusarium oxysporum isolate C34-294 Brazil (KJ439088) and had 89% similarity with sequence Fusarium oxysporum f.sp. fragariae China (KT833080). Homology levels were tested between sequences and showed that Candi Kuning sequence and Gobleg sequence had 95% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. While Pancasari sequence have 94% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. Candi Kuning, Gobleg, and Pancasari sequences had the same 86% with sequence of Fusarium oxysporum isolate C34-294 Brazil (KJ439088) and had 89% similarity with sequence Fusarium oxysporum f.sp. fragariae China (KT833080). Based on phylogeny analysis of Pancasari, Gobleg and Candi Kuning isolates were obtained in one group with Fusarium oxysporum identified in America and Brazil, and also in one group with Fusarium oxysporum f. sp. fragariae that identified in China.
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GEREMIA, Roberto A., E. Alejandro PETRONI, Luis IELPI, and Bernard HENRISSAT. "Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases." Biochemical Journal 318, no. 1 (August 15, 1996): 133–38. http://dx.doi.org/10.1042/bj3180133.
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A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].
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Drijver, Evert, Joep Stohr, Jaco Verweij, Carlo Verhulst, Francisca Velkers, Arjan Stegeman, Marjolein Bergh, Jan Kluytmans, and i.-Health Group. "Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands." Microorganisms 8, no. 11 (November 8, 2020): 1755. http://dx.doi.org/10.3390/microorganisms8111755.
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Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.
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Nasare, Kanchan, Amit Yadav, Anil K. Singh, K. B. Shivasharanappa, Y. S. Nerkar, and V. S. Reddy. "Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India." Plant Disease 91, no. 11 (November 2007): 1413–18. http://dx.doi.org/10.1094/pdis-91-11-1413.
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A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning and sequencing of the 16S rRNA and spacer regions were performed. Multiple sequence alignments of the 16S rRNA sequences revealed that they share very high sequence similarity with phytoplasmas of rice yellow dwarf, 16SrXI. However, the 16S-23S rRNA SR sequence analysis revealed that while the majority of phytoplasmas shared very high (>99%) sequence similarity with previously reported sugarcane phytoplasmas, two of them, namely BV2 (DQ380342) and VD7 (DQ380343), shared relatively low sequence similarity (79 and 84%, respectively). Therefore, these two phytoplasmas may be previously unreported ones that cause significant yield losses in sugarcane in India.
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G. S. Wijesiri, W. W. P. M. T. M. Karunasena,. "Application of Graph Theory in DNA similarity analysis of Evolutionary Closed Species." Psychology and Education Journal 58, no. 1 (January 1, 2021): 3428–34. http://dx.doi.org/10.17762/pae.v58i1.1282.
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DNA is a complex molecule that consists of biological information that is passed down from generation to generation. With the evolution over time, there are different kinds of species that evolved from a common ancestor because of the occurrence of DNA sequence rearrangements. DNA sequence similarity analysis is a major challenge since the number of sequences is rapidly increasing in the DNA database. In this research, we based a mathematical method to analyze the similarity of two DNA sequences using Graph Theory. This mathematical method started by modeling a weighted directed graph for each DNA sequence, constructing its adjacency matrix, and converting it to the representative vector for each graph. From these vectors, the similarity was determined by distance measurements such as Euclidean, Cosine, and Correlation. By keeping this method as the based method, we will check whether it is applicable for any DNA fragments in considered genomes and molecular similarity coefficients can be used as distance measurements. We will obtain similarities using the graph spectrum instead of the representative vector. Then we will compare the results from the representative vector and that of the graph spectrum. The modified method is tested by using the mitochondrial DNA of Human, Gorilla, and Orangutan. It gives the same result when the number of nucleotides in DNA fragments is increased.
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Su, Jie, and Junpeng Bao. "A Wavelet Transform Based Protein Sequence Similarity Model." Applied Mathematics & Information Sciences 7, no. 3 (May 1, 2013): 1103–10. http://dx.doi.org/10.12785/amis/070330.
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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Soo-Yong Kim, and Md Oliur Rahman. "Molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus inferred from analysis of internal transcribed spacer sequences." Bangladesh Journal of Plant Taxonomy 22, no. 2 (December 28, 2015): 111–18. http://dx.doi.org/10.3329/bjpt.v22i2.26072.
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The present study explored molecular phylogenetic analysis of 28 species of Euphorbia L. for the identification and establishment of molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus based on the internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA). The sequence similarity search using Basic Local Alignment Search Tool (BLAST) of the ITS sequence of E. scordifolia showed the closest sequence similarity to E. supina Raf. The analysis of ITS sequence data revealed four major clades consistent with subgeneric classifications of the genus. Molecular data support placement of E. scordifolia in the subgenus Chamaesyce.Bangladesh J. Plant Taxon. 22(2): 111-118, 2015 (December)
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Wilson, Clarke. "The Structure of Stages in the Evaluation Cycle: An Event Sequence Analysis." Canadian Journal of Program Evaluation 15, no. 1 (March 2000): 41–55. http://dx.doi.org/10.3138/cjpe.015.003.
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Abstract: From time to time, research on evaluation issues deals with a sequence of events or episodes which an analyst would prefer to examine in its entirety rather than event by event. However, quantitative methods for comparing sequences of events or activities and analyzing their similarity among populations and samples have rarely been applied in social research. This article describes the tasks undertaken during the cycle of evaluation of housing programs by CMHC prior to 1997 and analyses the major evaluation products in terms of the similarity of constituent tasks. A brief introduction to combinatorial methods for measuring similarities among whole character sequences is presented and new research applications are proposed. The analysis uses a new program for sequence alignment analysis called ClustalG, which is a modification of the ClustalX program used in molecular biology.
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Caputo, A., D. E. Sauer, and P. B. Rowe. "Nucleotide sequence and genomic organization of a human T lymphocyte serine protease gene." Journal of Immunology 145, no. 2 (July 15, 1990): 737–44. http://dx.doi.org/10.4049/jimmunol.145.2.737.
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Abstract We have determined the nucleotide sequence of 4508 base pairs of human genomic DNA which contain the human serine esterase gene from cytotoxic T lymphocytes (SECT) (equivalent to the 1-3E cDNA clone) and include 879 bp of 5' flanking DNA and 393 bp of 3' flanking DNA. The gene consists of five exons of 88, 148, 136, 261, and 257 nucleotides separated by four introns of 1043, 455, 205, and 643 nucleotides. The location of introns with respect to protein coding sequences in the SECT gene is identical to that of the human cathepsin G and murine granzyme B genes. Comparison of SECT gene exonic sequences to murine granzyme B-F cDNA sequences indicates similarities of 75 and 72% for granzymes B and C and 61, 59, and 61% for granzymes D, E, and F, respectively. The 5' flanking sequence of the SECT gene showed similarity only to the 5' flanking sequence of the murine granzyme B gene, indicating that these genes are homologous. Comparison of the SECT gene sequence to the human cathepsin G sequence indicated no similarity in the 5' flanking DNA although the exonic sequences show 64% sequence similarity overall and 45% sequence similarity in the respective 3' untranslated regions. These similarities suggest that the SECT and cathepsin G genes are members of the same family of serine protease genes. Evidence from high and low stringency Southern transfer analysis of human genomic DNA indicates the presence of another gene of at least 85% sequence similarity to the SECT gene.
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Thompson, F. L., D. Gevers, C. C. Thompson, P. Dawyndt, S. Naser, B. Hoste, C. B. Munn, and J. Swings. "Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis." Applied and Environmental Microbiology 71, no. 9 (September 2005): 5107–15. http://dx.doi.org/10.1128/aem.71.9.5107-5115.2005.
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ABSTRACT We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.
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Pereira, Maria das Graças C., Edward R. Atwill, Melissa R. Crawford, and Rance B. Lefebvre. "DNA Sequence Similarity between California Isolates of Cryptosporidium parvum." Applied and Environmental Microbiology 64, no. 4 (April 1, 1998): 1584–86. http://dx.doi.org/10.1128/aem.64.4.1584-1586.1998.
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ABSTRACT We evaluated whether nucleic acid amplification with primers specific for Cryptosporidium parvum followed by automated DNA sequence analysis of the PCR amplicons could differentiate between California isolates of C. parvum obtained from livestock, humans, and feral pigs. Almost complete sequence identity existed among the livestock isolates and between the livestock and human isolates. DNA sequences from feral pig isolates differed from those from livestock and humans by 1.0 to 1.2%. The reference sequence obtained by Laxer et al. (M. A. Laxer, B. K. Timblin, and R. J. Patel, Am. J. Trop. Med. Hyg. 45:688–694, 1991.) differed from California isolates of C. parvum by 1.8 to 3.2%. These data suggest that DNA sequence analysis of the amplicon of Laxer et al. does not allow for differentiation between various strains of C. parvum or that our collection of isolates obtained from various hosts from across California was limited to one strain ofC. parvum.
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Kholiq, Hibban, Mamika Ujianita Romdhini, and Marliadi Susanto. "Algoritma Needleman-Wunsch dalam Menentukan Tingkat Kemiripan Urutan DNA Rusa Timor (Cervus timorensis) dan Rusa Merah (Cervus elaphus)." EIGEN MATHEMATICS JOURNAL 3, no. 2 (December 30, 2020): 125. http://dx.doi.org/10.29303/emj.v3i2.65.
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Sequence alignment is a basic method in sequence analysis. This method is used to determine the similaritiy level of DNA sequences. The Needleman-Wunsch algorithm is an algorithm that can be used to solve the problem of sequence alignment. This research shows that the relation T (i, j) used in the Needleman-Wunsch algorithm is a function where T: (ℕ0 ℕ0) → ℤ. The function T (i, j) is a recursive function. Moreover, DNA sequence data used are DNA sequences from the Timor Deer, which are the identities of the provinces of West Nusa Tenggara and Red Deer, which are typical deer from the European continent as a comparison. The DNA sequence data was obtained from BLAST (Basic Local Alignment Search Tool). Based on the alignment, the most optimal alignment is obtained by forming 666 base pairs sequences with 322 matches, 230 missmatches and 114 gaps, meaning that the two DNA sequences have a 48% similarity (322/666).
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Powell, J. F., Y. P. Hsu, W. Weyler, S. Chen, J. Salach, K. Andrikopoulos, J. Mallet, and X. O. Breakefield. "The primary structure of bovine monoamine oxidase type A. Comparison with peptide sequences of bovine monoamine oxidase type B and other flavoenzymes." Biochemical Journal 259, no. 2 (April 15, 1989): 407–13. http://dx.doi.org/10.1042/bj2590407.
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We have isolated cDNA clones believed to encompass the full-length coding sequences for a subunit of bovine monoamine oxidase type A (MAO-A). The clones code for an apoprotein of 527 amino acid residues corresponding to a molecular mass of 59,806 Da. The inferred protein sequences show an overall similarity of 68% with partial amino acid sequences of bovine type B MAO (about 41% of the total sequence), as well as a greater similarity (greater than 90%) with some regions including that for the published sequence of the flavin-binding region. Sequence comparisons indicate that these two forms of MAO are encoded by distinct genes. Comparison of this sequence with other flavoenzymes showed similarity with regions associated with non-covalent flavin-binding sites. Analysis of mRNAs coding for MAO enzymes showed a heterogeneity of transcripts consistent with several different forms of monoamine oxidase.
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Gancheva, Veska, and Hristo Stoev. "Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment." Genes 15, no. 3 (March 7, 2024): 341. http://dx.doi.org/10.3390/genes15030341.
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Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of biological data. Sequence comparisons are the best way to investigate and understand the biological functions and evolutionary relationships between genes on the basis of the alignment of two or more DNA sequences in order to maximize the identity level and degree of similarity. This paper presents a new version of the pairwise DNA sequences alignment algorithm, based on a new method called CAT, where a dependency with a previous match and the closest neighbor are taken into consideration to increase the uniqueness of the CAT profile and to reduce possible collisions, i.e., two or more sequence with the same CAT profiles. This makes the proposed algorithm suitable for finding the exact match of a concrete DNA sequence in a large set of DNA data faster. In order to enable the usage of the profiles as sequence metadata, CAT profiles are generated once prior to data uploading to the database. The proposed algorithm consists of two main stages: CAT profile calculation depending on the chosen benchmark sequences and sequence comparison by using the calculated CAT profiles. Improvements in the generation of the CAT profiles are detailed and described in this paper. Block schemes, pseudo code tables, and figures were updated according to the proposed new version and experimental results. Experiments were carried out using the new version of the CAT method for DNA sequence alignment and different datasets. New experimental results regarding collisions, speed, and efficiency of the suggested new implementation are presented. Experiments related to the performance comparison with Needleman–Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. A performance analysis of the proposed algorithm based on the CAT method against the Knuth–Morris–Pratt algorithm, which has a complexity of O(n) and is widely used for biological data searching, was performed. The impact of prior matching dependencies on uniqueness for generated CAT profiles is investigated. The experimental results from sequence alignment demonstrate that the proposed CAT method-based algorithm exhibits minimal deviation, which can be deemed negligible if such deviation is considered permissible in favor of enhanced performance. It should be noted that the performance of the CAT algorithm in terms of execution time remains stable, unaffected by the length of the analyzed sequences. Hence, the primary benefit of the suggested approach lies in its rapid processing capabilities in large-scale sequence alignment, a task that traditional exact algorithms would require significantly more time to perform.
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Killer, J., J. Kopečný, J. Mrázek, I. Koppová, J. Havlík, O. Benada, and T. Kott. "Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract." International Journal of Systematic and Evolutionary Microbiology 61, no. 6 (June 1, 2011): 1315–21. http://dx.doi.org/10.1099/ijs.0.022525-0.
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Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866T, B. indicum JCM 1302T and B. coryneforme ATCC 25911T (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097T and B. coryneforme ATCC 25911T (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2T = DSM 22766T = CCM 7728T) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4T = DSM 22767T = CCM 7729T).
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Yang, Tae-Jin, Jung-Sun Kim, Ki-Byung Lim, Soo-Jin Kwon, Jin-A. Kim, Mina Jin, Jee Young Park, et al. "The KoreaBrassicaGenome Project: a Glimpse of theBrassicaGenome Based on Comparative Genome Analysis WithArabidopsis." Comparative and Functional Genomics 6, no. 3 (2005): 138–46. http://dx.doi.org/10.1002/cfg.465.
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A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) ofBrassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones fromBrassicachromosome 1 revealed their homeologous partner regions on theArabidopsisgenome and a syntenic comparative map betweenBrassicachromosome 1 andArabidopsischromosomes.In silicochromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (peri)centromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and anArabidopsischromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that theBrassicagenome has undergone triplication and subsequent gene losses after the divergence ofArabidopsisandBrassica. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering theBrassicagenome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100 000 BAC clones. The sequences have been submitted to GenBank with accession numbers: 10 204 BAC ends of the KBrH library (CW978640–CW988843); KBrH138P04, AC155338; KBrH117N09, AC155337; KBrH097M21, AC155348; KBrH093K03, AC155347; KBrH081N08, AC155346; KBrH080L24, AC155345; KBrH077A05, AC155343; KBrH020D15, AC155340; KBrH015H17, AC155339; KBrH001H24, AC155335; KBrH080A08, AC155344; KBrH004D11, AC155341; KBrH117M18, AC146875; KBrH052O08, AC155342.
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Bux, Bhagwan, Pankaj Kumar, Mahesh Kumar Bharti, and Jitender Singh. "Molecular Characterization of Proline Rich Regions in Lens culinaris under Abiotic Stress." International Journal of Bio-resource and Stress Management 13, no. 6 (June 30, 2022): 638–45. http://dx.doi.org/10.23910/1.2022.2935a.
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The present study attempt was made to isolate and characterized Lens culinaris full length proline rich gene. EST Sequences of proline gene (GT-622346.1) from Lens culinaris was retrieved from Genbank. This sequence was used as query against chickpea. Similarity sequence search has shown up to 90% similarity with EST sequence of chickpea having the Accession No. GR 398344 and up to 85% similarity with EST sequence having Accession No. GT 622346 of Lens culinaris. The positive results were subjected to sequencing and were further in-silico analysis carried out. BLASTp of the lentil sequence showed 98% similarity with Phaseolus vulgaris (accession number-CAJ43592), 97% with Cicer arietinum (accession number-XP004506458), 96% with Medicago truncatula (accession number-Q40375) and 91% similarity with Pisum sativum (accession number-CAB63486). Ten conserved repeats of 180 amino acids each in case of Lens culinaris having the repeat sequence “KPPVEKPPVY” was observed. The sequence was further translated into amino acid sequence and the Interproscan results for proline rich protein in Lens culinaris was found. These findings may help to develop more tolerant lentil crop against drought having a higher potential to satisfy demands for production by increasing the crop productivity.
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Mohanta, Tapan Kumar. "Corona virus (CoVid19) genome: genomic and biochemical analysis revealed its possible synthetic origin." Journal of Applied Biotechnology & Bioengineering 7, no. 5 (2020): 200–213. http://dx.doi.org/10.15406/jabb.2020.07.00235.
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The Severe acute respiratory syndrome (SARS) corona virus 2 SARS-CoV-2 mediated epidemic is a global pandemic. It has evolved as a curse to the human civilization and at the present situation, where most of the cities in the world are on lockdown. The first genome sequence data of SARS-CoV-2 (CoVid19) and their reports that followed concluded that it was a member of the genus Betacoronavirus and has a bat reservoir. To understand its origin and evolution, we conducted a deep comparative study by comparing the genomes of bat SARS CoV and other SARS CoVs (including human SARS CoV of German isolate). Results revealed that CoVid19 genomes from isolates of China, India, Italy, Nepal, and the United States of America has sequence similarity of 79-80% only with the bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV of German isolate. Whereas, the sequence similarity within the CoVid19 genomes of these countries was 99-100%. If the SARS CoV infection happened to human through the SARS CoV of bat origin, it should have sequence similarity of more than 99% which was absent in this case. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV of China, India, Italy, Nepal, and USA isolates. The genome analysis revealed the presence of multiple microsatellite repeats sequences. Proteome analysis revealed, the melting temperature (Tm) of surface glycoprotein was less than 55oC, suggesting the steam treatment can be an ideal preventative measure to destabilize the CoVid19, and thus it’s spreading
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Xu, Pan, An Chun Cheng, Ming Shu Wang, De Kang Zhu, and Xiao Jia Wang. "Sequence Analysis of the Riemerella anatipestifer OmpAMotB Gene(ORF 648bp) by Bioinformatics." Advanced Materials Research 647 (January 2013): 381–85. http://dx.doi.org/10.4028/www.scientific.net/amr.647.381.
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The OmpA/MotB gene from RA by our lab was sequenced. And the molecular characteristic of this gene was analyzed with bioinformatics software. The result indicated that an open reading frame(ORF) containing 648bp nucleotides was preliminarily identified by aligning with gene bank database by software of BlastN and ORF Finder. The GC content of RA OmpA/MotB gene was 36.88% and encoded a 215 amino acids in this peptide. And from the analysis results we know that this gene sequence didn’t contain a successive at least two rare codons string. Phylogenetic tree of the amino acids sequences showed this gene has not very high similarity with the other 15 OmpA/MotB protein sequence.
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Beccari, T., J. Hoade, A. Orlacchio, and J. L. Stirling. "Cloning and sequence analysis of a cDNA encoding the α-subunit of mouse β-N-acetylhexosaminidase and comparison with the human enzyme." Biochemical Journal 285, no. 2 (July 15, 1992): 593–96. http://dx.doi.org/10.1042/bj2850593.
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cDNAs encoding the mouse beta-N-acetylhexosaminidase alpha-subunit were isolated from a mouse testis library. The longest of these (1.7 kb) was sequenced and showed 83% similarity with the human alpha-subunit cDNA sequence. The 5′ end of the coding sequence was obtained from a genomic DNA clone. Alignment of the human and mouse sequences showed that all three putative N-glycosylation sites are conserved, but that the mouse alpha-subunit has an additional site towards the C-terminus. All eight cysteines in the human sequence are conserved in the mouse. There are an additional two cysteines in the mouse alpha-subunit signal peptide. All amino acids affected in Tay-Sachs-disease mutations are conserved in the mouse.
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Michalek, Wolfgang, Gottfried Künzel, and Andreas Graner. "Sequence analysis and gene identification in a set of mapped RFLP markers in barley (Hordeum vulgare)." Genome 42, no. 5 (October 1, 1999): 849–53. http://dx.doi.org/10.1139/g99-036.
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The "Igri/Franka" (I/F) map ranks among the most comprehensive genetic linkage maps of barley (Hordeum vulgare), containing a large number of markers derived from cDNA and genomic PstI clones. Fourty-three cDNA clones and 259 genomic clones were at least partially sequenced and compared with the major data bases of protein and nucleic acid sequences. Of the cDNA clones, 53% show significant similarity to known sequences in protein data bases. A comparison of sequences from genomic clones to nucleic acid sequence data bases revealed similarities for 9% of the clones. For cDNA sequences analyzed the same way, significant similarities were observed for 35% of the clones. These results show that genomic PstI clones, although containing genes at a significant frequency, represent an inappropriate source for an efficient, systematic gene identification in barley. Sequence information obtained in the context of the present study provides a resource for the conversion of these markers into sequence-tagged site (STS) markers and their use in PCR assays.Key words: data base comparison, DNA probe, gene identification, STS marker.
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POPESCU, D., IONELA MIRELA NEAGOE, SUZANA E. CILIEVICI, DIANA R. CONSTANTIN, and V. I. R. NICULESCU. "ANALYSIS OF THE CRYPTOSPORIDIUM SPP GP60 GENE VARIABILITY APPLYING INFORMATION THEORY." Romanian Journal of Biophysics 34, no. 1 (February 27, 2024): 1–12. http://dx.doi.org/10.59277/rjb.2024.1.01.
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In this paper we used statistical methods to understand the genetic information of DNA considered as a statistical system. The alphabet of a DNA sequence is defined by the four nucleotides: adenine, cytosine, guanine, and thymine. The order of nucleotides along the DNA sequences encodes the genetic information. We have analyzed three Cryptosporidium DNA sequences: one DNA sequence isolated and analyzed in our laboratory and two DNA reference sequences from the public database GenBank. Each DNA sequence is considered as a statistical system and is represented by a random variable and an associate probability distribution. The Shannon entropy, Renyi entropy, Onicescu informational energy and square deviation from uniform distribution are used in order to measure the degree of randomness for the three statistical systems. The similarity and difference between the three DNA sequences of the two Cryptosporidium species (Cryptosporidium hominis and Cryptosporidium parvum) were assessed by calculating the statistical distance between the probability distributions associated with each pair of DNA sequences. Each of the three DNA sequences pairs with one of the other two sequences and forms three pairs of sequences. Using the associated probability distributions, the statistical distance between them can be calculated. Bhattacharyya distance measures similarity degree between the two probability distributions. The Kullback-Leiber and the resistor-average distances measure the difference between the two distributions.
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Abd Elwahaab, Marwa A., Mervat M. Abo-Elkhier, and Moheb I. Abo el Maaty. "A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector." BioMed Research International 2019 (May 8, 2019): 1–9. http://dx.doi.org/10.1155/2019/8702968.
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Similarity/dissimilarity analysis is a key way of understanding the biology of an organism by knowing the origin of the new genes/sequences. Sequence data are grouped in terms of biological relationships. The number of sequences related to any group is susceptible to be increased every day. All the present alignment-free methods approve the utility of their approaches by producing a similarity/dissimilarity matrix. Although this matrix is clear, it measures the degree of similarity among sequences individually. In our work, a representative of each of three groups of protein sequences is introduced. A similarity/dissimilarity vector is evaluated instead of the ordinary similarity/dissimilarity matrix based on the group representative. The approach is applied on three selected groups of protein sequences: beta globin, NADH dehydrogenase subunit 5 (ND5), and spike protein sequences. A cross-grouping comparison is produced to ensure the singularity of each group. A qualitative comparison between our approach, previous articles, and the phylogenetic tree of these protein sequences proved the utility of our approach.
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Barik, Sasmita, Chandra Mohan Sidappa, Mohini Saini, Ramesh Doreswamy, Asit Das, Anil K. Sharma, and Praveen K. Gupta. "Sequence-Based Appraisal of the Genes Encoding Neck and Carbohydrate Recognition Domain of Conglutinin in Blackbuck (Antilope cervicapra) and Goat (Capra hircus)." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/389150.
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Conglutinin, a collagenous C-type lectin, acts as soluble pattern recognition receptor (PRR) in recognition of pathogens. In the present study, genes encoding neck and carbohydrate recognition domain (NCRD) of conglutinin in goat and blackbuck were amplified, cloned, and sequenced. The obtained 488 bp ORFs encoding NCRD were submitted to NCBI with accession numbers KC505182 and KC505183. Both nucleotide and predicted amino acid sequences were analysed with sequences of other ruminants retrieved from NCBI GenBank using DNAstar and Megalign5.2 software. Sequence analysis revealed maximum similarity of blackbuck sequence with wild ruminants like nilgai and buffalo, whereas goat sequence displayed maximum similarity with sheep sequence at both nucleotide and amino acid level. Phylogenetic analysis further indicated clear divergence of wild ruminants from the domestic ruminants in separate clusters. The predicted secondary structures of NCRD protein in goat and blackbuck using SWISSMODEL ProtParam online software were found to possess 6 beta-sheets and 3 alpha-helices which are identical to the result obtained in case of sheep, cattle, buffalo, and nilgai. However, quaternary structure in goat, sheep, and cattle was found to differ from that of buffalo, nilgai, and blackbuck, suggesting a probable variation in the efficiency of antimicrobial activity among wild and domestic ruminants.
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Bellachioma, G., J. L. Stirling, A. Orlacchio, and T. Beccari. "Cloning and sequence analysis of a cDNA clone coding for the mouse GM2 activator protein." Biochemical Journal 294, no. 1 (August 15, 1993): 227–30. http://dx.doi.org/10.1042/bj2940227.
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A cDNA (1.1 kb) containing the complete coding sequence for the mouse GM2 activator protein was isolated from a mouse macrophage library using a cDNA for the human protein as a probe. There was a single ATG located 12 bp from the 5‘ end of the cDNA clone followed by an open reading frame of 579 bp. Northern blot analysis of mouse macrophage RNA showed that there was a single band with a mobility corresponding to a size of 2.3 kb. We deduce from this that the mouse mRNA, in common with the mRNA for the human GM2 activator protein, has a long 3′ untranslated sequence of approx. 1.7 kb. Alignment of the mouse and human deduced amino acid sequences showed 68% identity overall and 75% identity for the sequence on the C-terminal side of the first 31 residues, which in the human GM2 activator protein contains the signal peptide. Hydropathicity plots showed great similarity between the mouse and human sequences even in regions of low sequence similarity. There is a single N-glycosylation site in the mouse GM2 activator protein sequence (Asn151-Phe-Thr) which differs in its location from the single site reported in the human GM2 activator protein sequence (Asn63-Val-Thr).
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Duffy, Simon P., Aaron M. Young, Benoit Morin, Christopher J. Lucarotti, Ben F. Koop, and David B. Levin. "Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome." Journal of Virology 80, no. 14 (July 15, 2006): 6952–63. http://dx.doi.org/10.1128/jvi.00187-06.
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ABSTRACT Of 30 baculovirus genomes that have been sequenced to date, the only nonlepidopteran baculoviruses include the dipteran Culex nigripalpus nucleopolyhedrovirus and two hymenopteran nucleopolyhedroviruses that infect the sawflies Neodiprion lecontei (NeleNPV) and Neodiprion sertifer (NeseNPV). This study provides a complete sequence and genome analysis of the nucleopolyhedrovirus that infects the balsam fir sawfly Neodiprion abietis (Hymenoptera, Symphyta, Diprionidae). The N. abietis nucleopolyhedrovirus (NeabNPV) is 84,264 bp in size, with a G+C content of 33.5%, and contains 93 predicted open reading frames (ORFs). Eleven predicted ORFs are unique to this baculovirus, 10 ORFs have a putative sequence homologue in the NeleNPV genome but not the NeseNPV genome, and 1 ORF (neab53) has a putative sequence homologue in the NeseNPV genome but not the NeleNPV genome. Specific repeat sequences are coincident with major genome rearrangements that distinguish NeabNPV and NeleNPV. Genes associated with these repeat regions encode a common amino acid motif, suggesting that they are a family of repeated contiguous gene clusters. Lepidopteran baculoviruses, similarly, have a family of repeated genes called the bro gene family. However, there is no significant sequence similarity between the NeabNPV and bro genes. Homologues of early-expressed genes such as ie-1 and lef-3 were absent in NeabNPV, as they are in the previously sequenced hymenopteran baculoviruses. Analyses of ORF upstream sequences identified potential temporally distinct genes on the basis of putative promoter elements.
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D'Hoostelaere, L. A., and D. Klinman. "Characterization of new mouse V kappa groups." Journal of Immunology 145, no. 8 (October 15, 1990): 2706–12. http://dx.doi.org/10.4049/jimmunol.145.8.2706.
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Abstract A lambda gt10 BXSB spleen cDNA library was screened with a DNA probe for the C kappa region. Forty individual C kappa+ phages were tested for hybridization with DNA probes representing 11 V kappa region groups. Of the phage inserts large enough to contain V kappa region sequences, 3 were negative for hybridization with all 11 V kappa region probes. The inserts from those three were subcloned, sequenced, and compared with V kappa region sequences in the gene bank. One was identical to 87.92.6 for the region sequenced (a member of V kappa RF). The second showed 93.8% sequence similarity with AN04 and called V kappa 32. The third called V kappa 33 showed 76% sequence similarity with the human sequence V52 and 73.2% sequence similarity with the mouse sequence L6. An insert from V kappa 32 containing the 5' untranslated regions through the codon for Cys 88 of the V kappa region was used as a probe in Southern blot analysis of genomic DNA from inbred and congenic strains of mice. V kappa 32 is a four to eight member group and some of the members are retained in the B6.PL-Ly2a congenic and missing from the B6.PL (85NS) congenic consistent with a map location near V kappa 28. The same filters were hybridized with the insert from V kappa 33 containing 5' untranslated region through the codon for Ser 93 of the V kappa region. V kappa 33 is a one to three member group and using the B6.PL congenics maps with the polymorphic fragments of V kappa 32 and V kappa 28.
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Asare, James Owusu, Justice Kwame Appati, and Kwaku Darkwah. "Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment." International Journal of Mathematics and Mathematical Sciences 2020 (June 1, 2020): 1–9. http://dx.doi.org/10.1155/2020/3858057.
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Global sequence alignment is one of the most basic pairwise sequence alignment procedures used in molecular biology to understand the similarity that arises among the structure, function, or evolutionary relationship between two nucleotide sequences. The general algorithm associated with global sequence alignment is the dynamic programming algorithm of Needleman and Wunsch. In this paper, patterns are exploited in the score matrix of the Needleman–Wunsch algorithm. With the help of some examples, the general patterns realized are formulated as new a priori propositions and corollaries that are established for both equal and unequal length comparisons of any two arbitrary sequences.
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Killer, J., I. Sedláček, V. Rada, J. Havlík, and J. Kopečný. "Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (November 1, 2013): 4350–53. http://dx.doi.org/10.1099/ijs.0.054957-0.
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The taxonomic position of Bifidobacterium stercoris Eg1T ( = JCM 15918T) based on comparative 16S rRNA gene and hsp60 sequence analyses was found to be controversial, as the strain showed high similarity to the type strain of Bifidobacterium adolescentis , CCUG 18363T. Therefore, the relationship between the two species was investigated by a taxonomic study that included, in addition to re-evaluation of the 16S rRNA gene sequence, determination of DNA–DNA binding and multilocus sequence analysis (MLSA) of housekeeping genes encoding the DNA-directed RNA polymerase B subunit (rpoC), putative xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp), elongation factor EF-G (fusA), 50S ribosomal protein L2 (rplB) and DNA gyrase B subunit (gyrB). Comparative 16S rRNA gene sequence analysis showed relatively high similarity (98.9 %) between B. stercoris KCTC 5756T and B. adolescentis ATCC 15703T. MLSA revealed close relatedness between B. stercoris KCTC 5756T and B. adolescentis CCUG 18363T, with 99.3–100 % similarity between the rpoC, xfp, fusA, rplB and gyrB gene sequences. In addition, relatively high dnaJ1 gene sequence similarity of 97.7 % was found between the strains. Similar phenotypes and a high DNA–DNA binding value (78.9 %) confirmed that B. stercoris and B. adolescentis are synonymous. Based on these results, it is proposed that the species Bifidobacterium stercoris Kim et al. 2010 should be reclassified as a later heterotypic synonym of Bifidobacterium adolescentis Reuter 1963 (Approved Lists 1980).
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Begum, RA, MT Alam, H. Jahan, and MS Alam. "Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh." Journal of Biodiversity Conservation and Bioresource Management 5, no. 1 (July 13, 2019): 25–30. http://dx.doi.org/10.3329/jbcbm.v5i1.42182.
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Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular.
J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30
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Wang, M. L., J. A. Mosjidis, J. B. Morris, R. E. Dean, T. M. Jenkins, and G. A. Pederson. "Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers." Genome 49, no. 6 (June 1, 2006): 707–15. http://dx.doi.org/10.1139/g06-027.
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The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.
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Gedela, Ravi, Naga Sai Babu Makke, and Dinesh Karra. "A Metagenomics Analysis on B-Carotene Synthesis in Neurospora Crassa." International Journal of Applied Sciences and Biotechnology 3, no. 3 (September 25, 2015): 490–503. http://dx.doi.org/10.3126/ijasbt.v3i3.13306.
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We have studied insilico on evolutionary uniqueness of phytoene synthase, which is one of the regulatory enzymes of ?-carotene synthesis in Neurospora crassa. This study reveals multiple sequence alignments showed high sequences with similarity within a species of bacteria, fungi and higher plants. This results designate interestingly between species of bacteria-fungi, fungi-plant, and among the species of bacteria-fungi-plant, showed tremendously less sequence with similarity, except bacteria-plant (high sequence with similarity) respectively. In Phylogenetics tree analysis showed within species of bacteria, fungi and plant 91%, 92% and 99% homology. Whereas in between species of bacteria-fungi, bacteria-plant, fungi-plant, and among the species bacteria-fungi-plant showed 99%, 96%, 100%, and 91%-99% homology respectively. N. crassa phytoene synthase enzyme encode (Isoprenoid Biosynthesis enzymes, Class 1) protein size 610aa, Cyanobacteria phytoene encode (Isoprenoid Biosynthesis enzymes, Class 1) protein size 310aa, and Oryza sativa Indica phytoene synthase 1 (chloroplast), (Isoprenoid Biosynthesis enzymes, Class 1) encode protein size 421aa (e- value 0.0, 0.0 and 0.0; identity 100%, 100% and 100%; Max.score:1238, 644 and 870) respectively. We studied insilico on basis of an evolutionary Endosymbiotic theory; a bacterium is the ancestors to eukaryotes. Int J Appl Sci Biotechnol, Vol 3(3): 490-503