Journal articles: 'Basic Local Alignment Search Tool'

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Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. "Basic local alignment search tool." Journal of Molecular Biology 215, no. 3 (October 1990): 403–10. http://dx.doi.org/10.1016/s0022-2836(05)80360-2.

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Mount, David W. "Using the Basic Local Alignment Search Tool (BLAST)." Cold Spring Harbor Protocols 2007, no. 7 (July 2007): pdb.top17. http://dx.doi.org/10.1101/pdb.top17.

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Wang, Hui, Leixiao Li, Chengdong Zhou, Hao Lin, and Dan Deng. "Spark-based Parallelization of Basic Local Alignment Search Tool." International Journal Bioautomation 24, no. 1 (March 2020): 87–98. http://dx.doi.org/10.7546/ijba.2020.24.1.000767.

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Eric, S. Donkor, T. K. D. Dayie Nicholas, and K. Adiku Theophilus. "Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)." Journal of Bioinformatics and Sequence Analysis 6, no. 1 (April 30, 2014): 1–6. http://dx.doi.org/10.5897/ijbc2013.0086.

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Konerding, D. "An Essential Guide to the Basic Local Alignment Search Tool: BLAST." Briefings in Bioinformatics 5, no. 1 (January 1, 2004): 93–94. http://dx.doi.org/10.1093/bib/5.1.93.

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O’Driscoll, Aisling, Vladislav Belogrudov, John Carroll, Kai Kropp, Paul Walsh, Peter Ghazal, and Roy D. Sleator. "HBLAST: Parallelised sequence similarity – A Hadoop MapReducable basic local alignment search tool." Journal of Biomedical Informatics 54 (April 2015): 58–64. http://dx.doi.org/10.1016/j.jbi.2015.01.008.

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Chen, Ying, Weicai Ye, Yongdong Zhang, and Yuesheng Xu. "High speed BLASTN: an accelerated MegaBLAST search tool." Nucleic Acids Research 43, no. 16 (2015): 7762–68. http://dx.doi.org/10.1093/nar/gkv784.

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Abstract Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

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Nowicki, Marek, Davit Bzhalava, and Piotr BaŁa. "Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library." Journal of Computational Biology 25, no. 8 (August 2018): 871–81. http://dx.doi.org/10.1089/cmb.2018.0079.

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Matsuda, Fumio, Hiroshi Tsugawa, and Eiichiro Fukusaki. "Method for Assessing the Statistical Significance of Mass Spectral Similarities Using Basic Local Alignment Search Tool Statistics." Analytical Chemistry 85, no. 17 (August 14, 2013): 8291–97. http://dx.doi.org/10.1021/ac401564v.

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Guo, Xinyu, Hong Wang, and Vijay Devabhaktuni. "A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm." ISRN Bioinformatics 2012 (September 4, 2012): 1–11. http://dx.doi.org/10.5402/2012/195658.

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A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. These implementations completed the first and second step of BLAST architecture and achieved significant speedup comparing with previously published architectures.

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Uthayakumar, Muthukumarasamy, Govindhan Sowmiya, Radhakrishnan Sabarinathan, N. Udayaprakash, M. Kirti Vaishnavi, and Kanagaraj Sekar. "BSSB:BLASTServer for Structural Biologists." Journal of Applied Crystallography 44, no. 3 (April 2, 2011): 651–54. http://dx.doi.org/10.1107/s0021889811008387.

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The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processingBLASToutput, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed toolBLASTServer for Structural Biologists (BSSB), which maps aBLASToutput onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence–structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

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Santelli, Roberto V., and Fábio Siviero. "A search for homologues of plant photoreceptor genes and their signaling partners in the sugarcane expressed sequence tag (Sucest) database." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 49–53. http://dx.doi.org/10.1590/s1415-47572001000100008.

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A search in the sugarcane expressed sequence tag (SUCEST) database for homologues of plant genes involved in photo-sensory mechanisms was carried out using the basic local alignment tool (BLAST). Our results shown that known elements (phytochromes, cryptochromes and phototoprin) present in Arabidopsis and other higher plants were detected with low e-values. We also searched for proteins interacting with photoreceptors in primary or downstream signaling events. One putative homologue for a protein postulated to be a primary element in phytochrome signaling pathways was identified, as were other candidates for downstream interacting factors.

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Brodmann, P. D., G. Nicholas, P. Schaltenbrand, and E. C. Ilg. "Identifying unknown game species: experience with nucleotide sequencing of the mitochondrial cytochrome b gene and a subsequent basic local alignment search tool search." European Food Research and Technology 212, no. 4 (March 7, 2001): 491–96. http://dx.doi.org/10.1007/s002170000284.

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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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West, Ruth, Jeff Burke, Cheryl Kerfeld, Eitan Mendelowitz, Thomas Holton, J. P. Lewis, Ethan Drucker, and Weihong Yan. "Both and Neither: in silico v1.0, Ecce Homology." Leonardo 38, no. 4 (August 2005): 286–93. http://dx.doi.org/10.1162/0024094054762089.

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Ecce Homology, a physically interactive new-media work, visualizes genetic data as calligraphic forms. A novel computer-vision user interface allows multiple participants, through their movement in the installation space, to select genes from the human genome for visualizing the Basic Local Alignment Search Tool (BLAST), a primary algorithm in comparative genomics. Ecce Homology was successfully installed in the UCLA Fowler Museum, 6 November 2003–4 January 2004.

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Oany, Arafat Rahman, Tahmina Pervin Jyoti, and Shah Adil Ishtiyaq Ahmad. "An in Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638)." Bioinformatics and Biology Insights 8 (January 2014): BBI.S14620. http://dx.doi.org/10.4137/bbi.s14620.

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Pyrococcus furiosus is a hyperthermophilic archaea. A hypothetical protein of this archaea, PF0847, was selected for computational analysis. Basic local alignment search tool and multiple sequence alignment (MSA) tool were employed to search for related proteins. Both the secondary and tertiary structure prediction were obtained for further analysis. Three-dimensional model was assessed by PROCHECK and QMEAN6 programs. To get insights about the physical and functional associations of the protein, STRING network analysis was performed. Binding of the SAM (S-adenosyl-1-methionine) ligand with our protein, fetched from an antibiotic-related methyltransferase (PDB code: 3P2K: D), showed high docking energy and suggested the function of the protein as methyltransferase. Finally, we tried to look for a specific function of the proposed methyltransferase, and binding of the geneticin bound to the eubacterial 16S rRNA A-site (PDB code: 1MWL) in the active site of the PF0847 gave us the indication to predict the protein responsible for aminoglycoside antibiotic resistance.

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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Gábor Gyulai, and Arun K. Pandey. "Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan." Bangladesh Journal of Plant Taxonomy 21, no. 1 (June 23, 2014): 33–42. http://dx.doi.org/10.3329/bjpt.v21i1.19256.

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The present study explored the use of internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA) for identification of Echinops mandavillei Kit Tan, an endemic species to Saudi Arabia. The sequence similarity search using Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses of the ITS sequence of E. mandavillei Kit Tan showed high level of sequence similarity (98%) with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. mandavillei could have a potential use for molecular genotyping.DOI: http://dx.doi.org/10.3329/bjpt.v21i1.19256Bangladesh J. Plant Taxon. 21(1): 33-42, 2014 (June)

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Ali, M. Ajmal, Fahad M. Al-Hemaid, Ritesh K. Choudhary, Joongku Lee, Soo-Yong Kim, and M. A. Rub. "Status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae) inferred from combined nuclear ribosomal and chloroplast sequence data." Bangladesh Journal of Plant Taxonomy 20, no. 2 (December 22, 2013): 233–38. http://dx.doi.org/10.3329/bjpt.v20i2.17397.

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The present study focuses on the status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae). The internal transcribed spacer (ITS) region of nuclear ribosomal DNA and chloroplast trnL-F gene of the questioned species were sequenced. The Basic Local Alignment Search Tool (BLAST) search showed maximum identity with R. stenostachya. The parsimony analysis of ITS, trnL-F and combined sequences data analyses revealed grouping of Reseda species consistent with established taxonomic sections of the genus, R. pentagyna showed proximity with R. stenostachya (100% bootstrap support), nested within the clade of section Reseda.DOI: http://dx.doi.org/10.3329/bjpt.v20i2.17397Bangladesh J. Plant Taxon. 20(2): 233-238, 2013

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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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Hentabli, Hamza, Faisal Saeed, Ammar Abdo, and Naomie Salim. "A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule." Scientific World Journal 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/286974.

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Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried.

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Seong, Eun Soo, Ji Hye Yoo, Jae Hoo Choi, Chang Heum Kim, Mi Ran Jeon, Byeong Ju Kang, Jae Geun Lee, Seon Kang Choi, Bimal Kumar Ghimire, and Chang Yeon Yu. "Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library inPerilla frutescens(L.)." International Journal of Genomics 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/679548.

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Perilla frutescensis valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses ofP. frutescensare limited due to a lack of gene annotations and characterization. A full-length cDNA library fromP. frutescensleaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers fromP. frutescenswill help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.

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Terai, Masanori, and Robert D. Burk. "Characterization of a novel genital human papillomavirus by overlapping PCR: candHPV86 identified in cervicovaginal cells of a woman with cervical neoplasia." Journal of General Virology 82, no. 9 (September 1, 2001): 2035–40. http://dx.doi.org/10.1099/0022-1317-82-9-2035.

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A novel human papillomavirus (HPV), candHPV86, was cloned and characterized from cervicovaginal cells obtained from a 37-year-old Hispanic woman with cervical intraepithelial neoplasia grade 1 (CIN1) using an overlapping PCR technique. Primers were designed by phylogenetic alignment of closely related HPV genomes using the L1 fragment sequence amplified by GP5+/6+. The 7983 bp complete nucleotide sequence of the HPV genome was determined by sequence walking. A basic local alignment sequence tool (BLAST) homology search using the L1 open reading frame demonstrated that this HPV was most closely related to HPVHAN2294 (GenBank, AJ400628; 86% homology) and HPV84 (84% homology). candHPV86 was placed in the HPV genome homology group A3 by phylogenetic analyses. The overlapping PCR technique is applicable for characterizing the complete spectrum and variation of HPVs in a population.

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De Oliveira Andrade, Luis Jesuino, Gustavo Magno Baptista, Juliane Santos Dias, Alcina Maria Vinhaes Bittencourt, and Larissa Santos França. "Relationship between vitiligo and Hashimoto's thyroiditis." Revista de Ciências Médicas e Biológicas 16, no. 1 (July 14, 2017): 5. http://dx.doi.org/10.9771/cmbio.v16i1.17619.

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Background: Vitiligo is a multifactorial acquired depigmenting disorder, characterized by a spontaneous loss of functional melanocytes from the epidermis. Vitiligo and Hashimoto's thyroiditis (HT) often occur in association and seem to be characterized by an autoimmune process. The vitiligo associated with HT suggests genetic homologies between them.Objective: To identify protein sequence homology between melanocyte protein (Pmel) and thyroid peroxidase (TPO), using bioinformatics tools, to propose an initial mechanism which could explain the production of cross-reacting autoantibodies to melanocyte and TPO.Methods: We performed a comparison between Pmel and TPO amino acids (AA) sequences, available on the National Center for Biotechnology Information (NCBI) database by BLAST (Basic Local Alignment Search Tool) in order to find local homology regions between the AA sequences.Results: The homology sequence between the Pmel and TPO ranged from 21.0 % (19 identical residues out of 90 AA in the sequence) to 55.0% (6 identical residues out of 11 AA in the sequence). The identical alignments presented relatively high E values due to presence of short alignment.Conclusion: Bioinformatics data suggest a possible pathological link between Pmel and TPO. Sequence homology between Pmel and TPO may present a molecular mimicry suggesting the possibility of antigen crossover between Pmel and TPO that might represent an immunological basis for vitiligo associated with HT.

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Shabaan, Amr M., Magdy M. Mohamed, Mohga S. Abdallah, Hayat M. Ibrahim, and Amr M. Karim. "Analysis of Schistosoma mansoni genes using the expressed sequence tag approach." Acta Biochimica Polonica 50, no. 1 (March 31, 2003): 259–68. http://dx.doi.org/10.18388/abp.2003_3735.

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Expressed sequence tags (ESTs) are partial cDNA sequences read from both ends of random expressed gene fragments used for discovering new genes. DNA libraries from four different developmental stages of Schistosoma mansoni used in this study generated 141 ESTs representing about 2.5% of S. mansoni sequences in dbEST. Sequencing was done by the dideoxy chain termination method. The sequences were submitted to GenBank for homology searching in nonredundant databases using Basic Local Alignment Search Tool for DNA (BLASTN) alignment and for protein (BLASTX) alignment at the National Center for Biotechnology Information (NCBI). Among submitted ESTs, 29 were derived from lambdagt11 sporocyst library, 70 from lambdaZap adult worm library, 31 from lambdaZap cercarial library, and 11 from lambdaZap female B worm library. Homology search revealed that eight (5.6%) ESTs shared homology to previously identified S.mansoni genes in dbEST, 15 (10.6%) are homologous to known genes in other organisms, 116 (81.7%) showed no significant sequence homology in the databases, and the remaining sequences (2.1%) showed low homologies to rRNA or mitochondrial DNA sequences. Thus, among the 141 ESTs studied, 116 sequences are derived from noval, uncharactarized S. mansoni genes. Those 116 ESTs are important for identification of coding regions in the sequences, helping in mapping of schistosome genome, and identifying genes of immunological and pharmacological significance.

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Taariwuan, Marlin Bernadet, Jantje Ngangi, Yermia Mokosuli, and Sukmarayu Gedoan. "DNA Barcoding Dalugha (Cyrtosperma Merkusii) di Kepulauan Talaud dan Minahasa Selatan Berdasarkan Gen rbcL." JURNAL BIOS LOGOS 11, no. 2 (September 4, 2021): 134. http://dx.doi.org/10.35799/jbl.v11i2.34452.

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(Article History: Received June 28, 2021; Revised August 30, 2021; Accepted Sept 3, 2021) ABSTRAKDalugha (Cyrtospera merkusii (Hassk.)Schott) merupakan tanaman endemik Sulawesi Utara yang digunakan sebagai pangan alternatif (penganti beras). Penelitian ini bertujuan untuk membandingkan spesies daluga di Kepulauan Talaud dan Minahasa Selatan menggunakan DNA barcode gen rbcL (ribulose 1,5 bisphosphate carboxylase large). Perbandingan barcode DNA yang dilakukan pada empat sampel yang berbeda lokasi tersebut keduanya menghasilkan tingkat kesamaan 100% (identik). Dengan demikian, tidak ada variasi intra spesies yang ditemukan dari semua sampel yang ada. Selanjutnya, kemiripan sampel-sampel ini telusuri kemiripannya dengan kerabat terdekat yang tercatat di GenBank menggunakan BLAST (Basic Local Alignment Search Tool). Tanaman dalugha dalam penelitian ini memiliki kemiripan 99,82% dengan tumbuhan Anaphyllopsis americana (AM905753.1), dan kemiripannya 99,63% dengan Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), dan Podolasia stipitata (AM905752.1). Belum ada rekor sekuens DNA gen rbcL dari spesies ini yang dibisa dibandingkan di GenBank.Kata Kunci: Dalugha; DNA barcoding; gen rbcL ABSTRACTDalugha (Cyrtospera merkusii (Hassk.) Schott) is an endemic plant in North Sulawesi that is used as alternative food (substitute for rice). This research aimed to compare the DNA barcode of dalugha in Talaud Islands and in South Minahasa using rbcL (ribulose 1,5 bisphosphate carboxylase large) gene. The DNA barcoding comparison of all four samples in both area resulted in 100% similarity (identical). Therefore, there is no intraspecific variation found in all samples. Furthermore, the similarity of these samples were conducted with BLAST (Basic Local Alignment Search Tool) to compare with its closest relatives in GenBank. The closest relatives of this plant, based on similarity information, are 99.82% with Anaphyllopsis americana (AM905753.1) and all 99.63% with Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), and Podolasia stipitata (AM905752.1). There is no record yet of rbcL gene sequence of C. merkusii in GenBank for comparison.Keywords: Dalugha; DNA barcoding; rbcL gene

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Chen, Xin, Li Xu, Xiao-juan Zong, Hai-rong Wei, Jia-wei Wang, Dong-zi Zhu, Yue Tan, Mao-run Fu, and Qing-zhong Liu. "Transcriptome Analysis, Marker Discovery and Pigment Biosynthesis of Red-leaf Juglans regia." Journal of Applied Biotechnology 5, no. 2 (June 4, 2017): 20. http://dx.doi.org/10.5296/jab.v5i2.11345.

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Red-leaf trait rarely occurs in Juglans regia, and the genetic mechanism underlying this phenomenon is still unknown. In this study, we attempted to provide insight into the comprehensive transcriptome of red-leaf J. regia by RNA-Seq using Illumina SeqTM2000 platform. A total of 33,488,602 high-quality reads (3.35G cleans bases) were obtained and assembled into 53,782 unigenes. A total of 3,683 unigenes were annotated by using basic local alignment search tool to search against protein databases, All the matched unigenes were categorized by gene ontology analysis, and 3,466 were assigned to metabolism, among which 74 were mapped to anthocyanin, carotenoid, and betalain biosynthetic pathways by Kyoto Encyclopedia of Genes and Genomes analysis. Approximately 656 transcription factors were isolated including MYB, NAC, and bHLH. Additionally, a total of 13,981 simple sequence repeats, 41,088 single nucleotide polymorphisms, and 5,860 insertions and deletions were determined from J. regia transcriptome. Therefore, the current J. regia transcriptome provides deep insight into the molecular basis of red-leaf breeding of J. regia.

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Dias, R., M. G. Xavier, F. D. Rossi, M. V. Neves, T. A. P. Lange, A. Giongo, C. A. F. De Rose, and E. W. Triplett. "MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment." Journal of Bioinformatics and Computational Biology 12, no. 03 (June 2014): 1450013. http://dx.doi.org/10.1142/s0219720014500139.

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Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min.

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Saleky, Dandi, and Sendy Lely Merly. "Molecular Phylogenetic of Cerithidea anticipata (Iredale, 1929) (Mollusk: Gastropod)." Jurnal Ilmiah PLATAX 9, no. 1 (February 10, 2021): 9. http://dx.doi.org/10.35800/jip.9.1.2021.32422.

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Species identification is very important and an important part of bioecological studies, so phylogenetic studies of Cerithidea anticipata (Iredale, 1929) was conducted in September 2020 to identify C. anticipata (Iredale, 1929) based on DNA barcoding techniques. Samples of C. anticipata (Iredale, 1929) were collected from the mangrove ecosystem of Payum Merauke Beach Papua (Indonesia), where the genes used were primary COI Gene forward LCO1490 and reverse HCO2198. The result of DNA amplification obtained DNA sequence length of 660 bp, then based on the identification of Basic Local Alignment Search Tools (BLAST) obtained a similarity level of 98.42% and phylogenetic reconstruction showed the existence of grouping based on the degree of similarity and genetic distance between populations.Keywords: Cerithidea anticipata; COI genes; DNA barcoding; phylogeneticsAbstrakIdentifikasi spesies sangat penting dilakukan dan menjadi bagian penting dalam studi bioekologi, sehingga kajian filogenetik Cerithidea anticipata (Iredale, 1929) telah dilakukan pada bulan September 2020 dengan tujuan untuk mengidentifikasi C. anticipata (Iredale, 1929) berdasarkan teknik DNA barcoding. Sampel C. anticipata (Iredale, 1929) dikoleksi dari ekosistem mangrove Pantai Payum Merauke Papua (Indonesia), dimana gen yang digunakan adalah Gen COI primer forward LCO1490 dan reverse HCO2198. Hasil dari amplifikasi DNA diperoleh panjang sekuen DNA 660 bp, kemudian berdasarkan identifikasi Basic Local Alignment Search Tools (BLAST) diperoleh tingkat kemiripannya 98.42% dan rekonstruksi filogenetiknya memperlihatkan adanya pengelompokan berdasarkan tingkat kemiripan maupun jarak genetik antar populasi.Kata kunci: Cerithidea anticipata; Gen COI; DNA barcoding; filogenetik

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Stevic, Nevena, Eleonora Capelja, Vladislava Galovic, Milana Novakovic, and Maja Karaman. "Molecular characterization of some lignicolous species from fungal culture collection." Genetika 46, no. 1 (2014): 235–42. http://dx.doi.org/10.2298/gensr1401235s.

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Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs) with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17) obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25?C. BLAST (Basic Local Alignment Search Tool) was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity.

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Yim, Won Cheol, and John C. Cushman. "Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments." PeerJ 5 (June 22, 2017): e3486. http://dx.doi.org/10.7717/peerj.3486.

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Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. This freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.

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Lorenzo, Consuelo, Jorge E. Bolaños-Citalán, and Oscar G. Retana-Guiascón. "Rediscovery of Heteromys nelsoni in its type locality after over a century." Mammalia 84, no. 1 (December 18, 2019): 6–9. http://dx.doi.org/10.1515/mammalia-2018-0154.

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Abstract We rediscovered a population of Nelson’s spiny pocket mouse (Heteromys nelsoni; Merriam, 1902) in the type locality of Pinabeto in the Mexican state of Chiapas, 121 years after it was last collected. We describe five topotype specimens according to their morphology and external measurements, and we confirm its identity at the species level in the Basic Local Alignment Search Tool (BLAST) of GenBank. As the population of H. nelsoni in Pinabeto is isolated, it is likely to be susceptible to extinction. There is a need to carry out additional scientific studies of this microendemic species in order to obtain more information regarding its biology, ecology and evolutionary history, and to be able to influence environmental policy to protect and conserve this species, as well as the region’s cloud forests.

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Tian, Hongling, Xiaoshuang Xu, Fusheng Zhang, Yaoqin Wang, Shuhong Guo, Xuemei Qin, and Guanhua Du. "Analysis ofPolygala tenuifoliaTranscriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing." International Journal of Genomics 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/782635.

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Radix polygalae, the dried roots ofPolygala tenuifoliaandP. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways ofP. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview ofP. tenuifoliatranscriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition ofP. tenuifoliamay be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications ofP. tenuifoliain pharmaceutical industries.

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Goldberg, Michael, Michelle Wei, Benjamin Tycko, Inna Falikovich, and Dorothy Warburton. "Identification and expression analysis of the human μ-protocadherin gene in fetal and adult kidneys." American Journal of Physiology-Renal Physiology 283, no. 3 (September 1, 2002): F454—F463. http://dx.doi.org/10.1152/ajprenal.00012.2002.

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We recently cloned μ-protocadherin, a developmentally regulated cell adhesion molecule that contains an extracellular region with four cadherin-like ectodomains and a triply repeating mucin domain in its longer isoform. Expression of μ-protocadherin in L929 cells resulted in cellular aggregation, confirming its role in intercellular adhesion. We now identify the human μ-protocadherin ortholog and study its distribution in vivo and its targeting in polarized epithelia. Basic Local Alignment Search Tool searches and fluorescent in situ hybridization analysis on the basis of human-mouse synteny reveal that μ-protocadherin maps to 11p15.5, matching a previously identified gene called MUCDHL. At least three different splicing isoforms exist for MUCDHL that vary in expression in the fetal kidney. μ-Protocadherin is apically expressed along the brush border of the proximal convoluted tubule of the adult kidney. Transfection of truncated forms of μ-protocadherin into polarized Madin-Darby canine kidney cells reveals that the NH2terminus is essential for targeting to the apical surface. These results suggest that although human μ-protocadherin may mediate a homotypic adhesive interaction, it may have additional functions in terminally differentiated epithelia.

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Lau, Joann M., and David L. Robinson. "Effectiveness of a Cloning and Sequencing Exercise on Student Learning with Subsequent Publication in the National Center for Biotechnology Information GenBank." CBE—Life Sciences Education 8, no. 4 (December 2009): 326–37. http://dx.doi.org/10.1187/cbe.09-05-0036.

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With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,” which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6- to 8-wk project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise.

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FLORES FERNÁNDEZ, JOSÉ MIGUEL, CARLA PATRICIA BARRAGÁN ÁLVAREZ, CARLA VANESSA SÁNCHEZ HERNÁNDEZ, EDUARDO PADILLA CAMBEROS, CELIA GONZÁLEZ CASTILLO, DANIEL ORTUÑO SAHAGÚN, and MOISÉS MARTÍNEZ VELÁZQUEZ. "Molecular characterization and expression analysis of three novel autophagy-related genes from the cattle tick Rhipicephalus (Boophilus) microplus (Acari: Ixodidae)." Parasitology 143, no. 13 (September 9, 2016): 1802–9. http://dx.doi.org/10.1017/s0031182016001542.

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SUMMARYThe cattle tick Rhipicephalus (Boophilus) microplus is a hematophagous ectoparasite of major importance for the livestock industry. It shows a remarkable ability to survive over long periods without feeding. However, the mechanisms used to endure long-term starvation are poorly understood. It is believed that autophagy, a process of intracellular protein degradation, may play a significant role to confront adverse environmental conditions. To advance our understanding of autophagy in R. microplus, in the present study we report the molecular characterization of three autophagy-related (ATG) genes, namely, RmATG3, RmATG4 and RmATG6, as well as their expression profiles in different developmental stages and organs of the parasite. The deduced amino acid sequences derived from the characterized gene sequences were subjected to Basic Local Alignment Search Tool analysis. The testing produced significant alignments with respective ATG proteins from Haemaphysalis longicornis and Ixodes scapularis ticks. Real-time polymerase chain reaction assays revealed that RmATG4 and RmATG6 transcripts were elevated in egg and ovary tissue, when compared with larva and midgut samples, while RmATG3 expression in midgut was 2-fold higher than in egg, larva and ovary samples.

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Jancso, Mario A., Susana A. Sculaccio, and Otavio H. Thiemann. "Identification of sugarcane genes involved in the purine synthesis pathway." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 251–55. http://dx.doi.org/10.1590/s1415-47572001000100033.

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Nucleotide synthesis is of central importance to all cells. In most organisms, the purine nucleotides are synthesized de novo from non-nucleotide precursors such as amino acids, ammonia and carbon dioxide. An understanding of the enzymes involved in sugarcane purine synthesis opens the possibility of using these enzymes as targets for chemicals which may be effective in combating phytopathogen. Such an approach has already been applied to several parasites and types of cancer. The strategy described in this paper was applied to identify sugarcane clusters for each step of the de novo purine synthesis pathway. Representative sequences of this pathway were chosen from the National Center for Biotechnology Information (NCBI) database and used to search the translated sugarcane expressed sequence tag (SUCEST) database using the available basic local alignment search tool (BLAST) facility. Retrieved clusters were further tested for the statistical significance of the alignment by an implementation (PRSS3) of the Monte Carlo shuffling algorithm calibrated using known protein sequences of divergent taxa along the phylogenetic tree. The sequences were compared to each other and to the sugarcane clusters selected using BLAST analysis, with the resulting table of p-values indicating the degree of divergence of each enzyme within different taxa and in relation to the sugarcane clusters. The results obtained by this strategy allowed us to identify the sugarcane proteins participating in the purine synthesis pathway.

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Kim, Ok-Sun, Yong-Joon Cho, Kihyun Lee, Seok-Hwan Yoon, Mincheol Kim, Hyunsoo Na, Sang-Cheol Park, et al. "Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species." International Journal of Systematic and Evolutionary Microbiology 62, Pt_3 (March 1, 2012): 716–21. http://dx.doi.org/10.1099/ijs.0.038075-0.

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Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.

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Khatun, Marjia, and Laila Anjuman Banu. "A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient." European Journal of Medical and Health Sciences 3, no. 2 (March 31, 2021): 19–21. http://dx.doi.org/10.24018/ejmed.2021.3.2.744.

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A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardian of the pediatric patient, socio-demographic data was collected. Isolation of DNA, quantitation and qualitation of DNA was ensured, polymerase chain reaction (PCR) was performed, the amplicons that was obtained from PCR; validated visually by gel electrophoresis methods; cycle sequencing was performed by Sanger sequencing. The chromatogram data that was obtained from Sanger sequencing was analyzed and compared with the National Center for Biotechnology Information database by Basic Local Alignment Search Tool search. Sanger sequencing revealed substitution (c.1051G>T) in the Sequence Tagged Site of the exon2 of Thyroid transcription factor 2 gene and this is new variants and not reported in National Center for Biotechnology Information database.

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Dwarka, Arvin, Cynthia M. Ross Friedman, Mairi E. MacKay, and Don Nelson. "Polymerase chain reaction identification of a female-specific genetic marker in Arceuthobium americanum (lodgepole pine dwarf mistletoe) and its implications for Arceuthobium sex determination." Botany 89, no. 6 (June 2011): 369–77. http://dx.doi.org/10.1139/b11-025.

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In North America, the most widespread and speciose mistletoe is Arceuthobium M. Bieb. (dwarf mistletoes, Viscaceae), which is a dioecious parasite of conifers. Little is known about its sex determination system, and sex chromosomes have not been identified. A genetic marker for early gender discrimination in Arceuthobium would be useful in the study of sex ratios and sex determination. Here, random amplified polymorphic DNA analysis via the polymerase chain reaction (PCR) was used to investigate genetic differences between genders in Arceuthobium americanum Nutt. ex Engelm. collected near Kamloops, British Columbia and Bélair, Manitoba. A total of 196 10-mer primers were selected for analysis of DNA from isolated male and female A. americanum somatic tissue. A ∼900 bp female-specific DNA fragment was generated with primer OPB-18 (5′-CCACAGCAGT-3′). The fragment was cloned and sequenced. Using GenBank and the basic local alignment search tool alignment software, it was determined that the first ∼300 bp of this DNA sequence shared a high degree of similarity to transposable elements (76%) and a Y-chromosome (male) fragment (75%) in Silene latifolia Poir. Sequence-characterized amplified region primers were then designed. This study has generated an efficient molecular tool to differentiate male and female A. americanum while also providing evidence indicating that A. americanum may have homomorphic, possibly protoheteromorphic, sex chromosomes.

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Kolondam, Beivy Jonathan. "Evaluasi Deteksi Berbasis PCR untuk Bakteri Bifidobacterium longum dalam Sampel Feses Bayi dari Kota Manado." JURNAL ILMIAH SAINS 20, no. 1 (April 6, 2020): 18. http://dx.doi.org/10.35799/jis.20.1.2020.27702.

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Bifidobakteria merupakan mikroflora yang umum hidup dalam usus manusia sejak bayi. Peran Bifidobacterium longum yang positif sebagai salah satu bakteri yang menunjang kesehatan inangnya membuat bakteri ini menjadi objek studi yang menarik. Salah satu instrumen dalam penelitian adalah adalah metode deteksi bakteri B. longum yang berbasis PCR (Polymerase Chain Reaction) gen 16S rRNA. Dengan mempertimbangkan bahwa perancangan primer untuk deteksi ini sudah lebih dari 20 tahun, penelitian ini bertujuan mengevaluasi hasil deteksi melalui PCR terhadap B. longum dalam feses bayi. Akurasi hasil dilihat melalui sekuensing terhadap hasil PCR sampel yang terdeteksi positif. Dua sampel feses bayi di Manado yang diperiksa menunjukkan hasil positif dan produk PCR tersebut dilakukan sekuensing. Panjang DNA yang nyata dari hasil deteksi ini yaitu 829 bp dan bukan 831 bp. Sekuens DNA kedua sampel ini identik satu sama lain. Hasil BLAST (Basic Local Alignment Search Tool) mengonfirmasi kesamaan 100% (identik) dari kedua specimen dari Kota Manado dengan sekuens gen 16S rRNA specimen bakteri B. longum yang telah ada dalam GenBank.Kata-kata kunci: Bifidobacterium longum, Polymerase Chain Reaction, deteksi, feses, bayi. Evaluation of PCR-Based Detection for Bifidobacterium longum in Infant Fecal Samples from Manado City ABSTRACTBifidobacteria are common members of the gut microflora of humans since infant. The Bifidobacterium longum has positive roles and one of supportive bacteria to the host, which made interesting as a study object. One instrument in studying this bacterial species is the detection method based on PCR of 16S rRNA gene. In consideration of the design of primers for this detection method is already more than 20 years, this research aimed to evaluate the PCR-based detection of B. longum in infant feces. The accuracy of the method was evaluated from sequencing of DNA fragment from positive results. Two fecal samples in Manado City shown positive result were sent for sequencing. The actual length of DNA amplified by PCR was 829 bp, not 831 bp. The DNA sequence of both samples were identical to each other. The BLAST (Basic Local Alignment Search Tool) result confirmed the similarity of both samples from Manado with 16S rRNA gene sequence of B. longum specimens in GenBank.Keywords: Bifidobacterium longum, Polymerase Chain Reaction, detection, feces, infant.

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Maynes, Jason T., Richard G. Yuan, and Floyd F. Snyder. "Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase." Journal of Bacteriology 182, no. 16 (August 15, 2000): 4658–60. http://dx.doi.org/10.1128/jb.182.16.4658-4660.2000.

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ABSTRACT Using the human cDNA sequence corresponding to guanine deaminase, the Escherichia coli genome was scanned using the Basic Local Alignment Search Tool (BLAST), and a corresponding 439-residue open reading frame of unknown function was identified as having 36% identity to the human protein. The putative gene was amplified, subcloned into the pMAL-c2 vector, expressed, purified, and characterized enzymatically. The 50.2-kDa protein catalyzed the conversion of guanine to xanthine, having a Km of 15 μM with guanine and a k cat of 3.2 s−1. The bacterial enzyme shares a nine-residue heavy metal binding site with human guanine deaminase, PG[FL]VDTHIH, and was found to contain approximately 1 mol of zinc per mol of subunit of protein. The E. coli guanine deaminase locus is 3′ from an open reading frame which shows homology to a bacterial purine base permease.

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Capelja, Eleonora, Nevena Stevic, Vladislava Galovic, Milana Novakovic, and Maja Karaman. "rDNA based analysis of autochtonous fungal species from Serbia." Genetika 46, no. 1 (2014): 33–42. http://dx.doi.org/10.2298/gensr1401033c.

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Determination of fungal species by traditional morphological approach can often be problematic. In the phylum Basidiomycota, sporocarps of different species can share very similar morphoanatomical characteristics. Using molecular markers and phylogenetic species concept this problem can be reduced. In this study identification of six autochtonous fungal species, collected from several locations in Serbia (Tara, Kopaonik, Stara planina) was done by comparison between morphological and molecular data of fungal species, as well as information obtained from phylogenetic tree. ITS sequences amplified from 11 specimens of two genera of ph. Basidiomycota: Marasmius and Ganoderma, were compared with ITS sequences from database using basic local alignment search tool (BLAST). Phylogenetic tree was constructed using Neighbor joining method based on differences between analyzed ITS sequences. Our results showed that within genera Marasmius and Ganoderma morphological and molecular determinations are usually in accordance, but for proper species delimitation both approaches should be used.

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Hajibaba, Majid, Mohsen Sharifi, and Saeid Gorgin. "The Influence of Memory-Aware Computation on Distributed BLAST." Current Bioinformatics 14, no. 2 (January 7, 2019): 157–63. http://dx.doi.org/10.2174/1574893613666180601080811.

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Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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Odronic, Shelley I., Thomas Scheidemantel, Marion J. Tuohy, Deborah Chute, Gary W. Procop, and Christine N. Booth. "Two Cases of Cokeromyces recurvatus in Liquid-Based Papanicolaou Tests and a Review of the Literature." Archives of Pathology & Laboratory Medicine 136, no. 12 (December 1, 2012): 1593–96. http://dx.doi.org/10.5858/arpa.2011-0493-cr.

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We present 2 cases of Cokeromyces recurvatus in routine, liquid-based Papanicolaou tests (ThinPrep). Patient 1 is a healthy, asymptomatic, 26-year-old woman with no pertinent past medical history. Patient 2 is a healthy, asymptomatic, 47-year-old woman with no pertinent past medical history. The Papanicolaou tests from both patients showed many fungal-like elements as globose, yeastlike forms measuring 10 to 30 µm in diameter with multiple, narrowly attached apparent “daughter” buds. This morphology was consistent with Paracoccidioides brasiliensis. However, broad-range fungal polymerase chain reaction and deoxyribonucleic acid sequence analysis performed with GenBank Basic Local Alignment Search Tool showed an exact match for C recurvatus. Our cases highlight the importance of molecular techniques to prevent misdiagnosis of C recurvatus as P brasiliensis, based on morphology alone. There have been 8 previously published cases of C recurvatus infection in humans, 3 of which were reported in the female genital tract.

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Kong, Liang, Lingfu Kong, and Rong Jing. "Improving the Prediction of Protein Structural Class for Low-Similarity Sequences by Incorporating Evolutionaryand Structural Information." Journal of Advanced Computational Intelligence and Intelligent Informatics 20, no. 3 (May 19, 2016): 402–11. http://dx.doi.org/10.20965/jaciii.2016.p0402.

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Protein structural class prediction is beneficial to study protein function, regulation and interactions. However, protein structural class prediction for low-similarity sequences (i.e., below 40% in pairwise sequence similarity) remains a challenging problem at present. In this study, a novel computational method is proposed to accurately predict protein structural class for low-similarity sequences. This method is based on support vector machine in conjunction with integrated features from evolutionary information generated with position specific iterative basic local alignment search tool (PSI-BLAST) and predicted secondary structure. Various prediction accuracies evaluated by the jackknife tests are reported on two widely-used low-similarity benchmark datasets (25PDB and 1189), reaching overall accuracies 89.3% and 87.9%, which are significantly higher than those achieved by state-of-the-art in protein structural class prediction. The experimental results suggest that our method could serve as an effective alternative to existing methods in protein structural classification, especially for low-similarity sequences.

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Toledo, Bethânia Figueiredo Barbosa de, Jackson Marcondes, and Eliana Gertrudes de Macedo Lemos. "Caracterização de rizóbios indicados para produção de inoculantes por meio de sequenciamento parcial do 16S rRNA." Pesquisa Agropecuária Brasileira 44, no. 4 (April 2009): 384–91. http://dx.doi.org/10.1590/s0100-204x2009000400008.

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O objetivo deste trabalho foi confrontar as sequências parciais do gene 16S rRNA de estirpes padrão de rizóbios com as de estirpes recomendadas para a produção de inoculantes no Brasil, com vistas à verificação da confiabilidade do sequenciamento parcial desse gene para a identificação rápida de estirpes. Foram realizados sequenciamentos através de reação em cadeia da polimerase (PCR) com iniciadores relativos à região codificadora do gene 16S rRNA entre as bactérias estudadas. Os resultados foram analisados pela consulta de similaridade de nucleotídeos aos do "Basic Local Alignment Search Tool" (Blastn) e por meio da interpretação de árvores filogenéticas geradas usando ferramentas de bioinformática. A classificação taxonômica das estirpes Semia recomendadas para inoculação de leguminosas com base em propriedades morfológicas e especificidade hospedeira não foi confirmada em todas as estirpes. A maioria das estirpes estudadas, consultadas no Blastn, é consistente com a classificação proposta pela construção de árvores filogenéticas das sequências destas estirpes, com base na similaridade pelo sequenciamento parcial do gene considerado.

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Valli S, Abiraami, and Mythili T. "BIOINFORMATIC STUDY OF AN ANTITUMOR PROTEIN, AZURIN." Asian Journal of Pharmaceutical and Clinical Research 11, no. 6 (June 7, 2018): 169. http://dx.doi.org/10.22159/ajpcr.2018.v11i6.23339.

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Objective: The main objective of this study is to analyze the structure and function of an antitumor protein, azurin, thereby giving validation to the protein structure and existing physicochemical properties in the anticancer protein which are responsible for the anticancer activity.Methods: Protein sequence analysis was done using Basic Local Alignment Search Tool (BLAST) with ten different randomly selected species of Pseudomonas obtained from GenBank. The physicochemical properties, prediction of secondary structure, identification of motifs and domains, three-dimensional (3-D) structure of the antitumor protein, validation through Ramachandran plot, multiple sequence alignment (MSA), and phylogenetic analysis were studied and functional property was confirmed through in silico docking.Results: The similarity search (BLAST-P analysis) for the primary sequence from GenBank carried out showed 86% similarity to the second sequence, azurin (Pseudomonas nitroreducens). The ProtParam, ExPASy tool server indicated the presence of essential physicochemical properties in azurin. Secondary structure prediction revealed random coil, extended strand, alpha helix, and beta turn. The study on domains indicated the presence of one domain in azurin responsible for the anticancer activity. The 3-D structural analysis revealed azurin as metalloprotein, of length-128, and polymer-1 with α-helices, β-sheets, and β-barrels. The validation carried out through Ramachandran plot showed the presence of two outliers (phi and psi). The biological relationship between the input sequences was studied through MSA and phylogenetic analysis. Further, azurin docked against the target protein (p53 tumor suppressor) showed the maximum binding affinity confirming its functional property of causing apoptosis.Conclusion: All the properties analyzed in the present study revealed that the azurin protein can act as a very good anticancer agent, and through the phylogenetic analysis, it was identified that Pseudomonas nitroreducens was closely related to the test organism Pseudomonas aeruginosa.

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Shiels, Browne, Donovan, Murray, and Saha. "Molecular Characterization of Twenty-Five Marine Cyanobacteria Isolated from Coastal Regions of Ireland." Biology 8, no. 3 (August 7, 2019): 59. http://dx.doi.org/10.3390/biology8030059.

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Twenty-five marine cyanobacteria isolated from Irish coasts were characterized based on their morphological characters and 16S rRNA gene sequence analysis. In addition, superoxide dismutase (SOD) and malate dehydrogenase (MDH) isoenzyme banding patterns were used to differentiate two morphologically ambiguous isolates. In this study, six new cyanobacteria-specific primers were designed, and a 16S rRNA gene of twenty-five morphologically diverse cyanobacteria was successfully PCR amplified (1198–1396 bps). Assembled 16S rRNA sequences were used both for a basic local alignment search tool (BLAST) analysis for genus-level identification and to generate a phylogenetic tree, which yielded two major clusters: One with morphologically homogenous cyanobacteria and the other with morphologically very diverse cyanobacteria. Kamptonema okenii and Tychonema decoloratum were isolated from a single field sample of Ballybunion and were originally identified as the same ‘Oscillatoria sp.’ based on preliminary morphological observations. However, an alignment of 16S rRNA gene sequences and SOD and MDH isoenzyme banding pattern analyses helped in differentiating the morphologically-indistinguishable ‘Oscillatoria sp.’. Finally, after a re-evaluation of their morphological characters using modern taxonomic publications, the originally identified ‘Oscillatoria sp.’ were re-identified as Kamptonema okenii and Tychonema decoloratum, thus supporting the polyphasic approach of cyanobacteria characterization.

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Amosova, Alexandra V., Lilit Ghukasyan, Olga Yu Yurkevich, Nadezhda L. Bolsheva, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk, and Olga V. Muravenko. "Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families." Plants 10, no. 6 (May 30, 2021): 1105. http://dx.doi.org/10.3390/plants10061105.

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The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.

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Rosa, Sarah Brena Aparecida, Bárbara Guimarães Csordas, Sandra Maria do Valle Leone de Oliveira, Amanda Ribeiro dos Santos, Anamaria Mello Miranda Paniago, and James Venturini. "Prediction of Conserved Peptides of Paracoccidioides for Interferon-γ Release Assay: The First Step in the Development of a Lab-Based Approach for Immunological Assessment during Antifungal Therapy." Journal of Fungi 6, no. 4 (December 19, 2020): 379. http://dx.doi.org/10.3390/jof6040379.

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Impaired antigen-specific cell-mediated immunity (CMI) is a primary immunological disturbance observed in individuals that develop paracoccidioidomycosis (PCM) after exposure to Paracoccidioides spp. Restoration of Paracoccidioides-specific CMI is crucial to stop the antifungal treatment and avoid relapses. A convenient and specific laboratory tool to assess antigen specific CMI is required for the appropriate clinical treatment of fungal infections, in order to decrease the time of antifungal therapy. We used an interferon-γ release assay strategy, used in the diagnosis of latent tuberculosis infection, to address our aims in this study. Information on proteins secreted by two well-studied representative strains—Paracoccidioides brasiliensis (Pb18) and P. lutzii (Pb-01)—were explored using PubMed or MEDLINE. From 26 publications, 252 proteins were identified, of which 203 were similar according to the Basic Local Alignment Search Tool. This enabled a selection of conserved peptides using the MEGA software. The SignalP-5.0, TMHMM, IEDB, NetMHC II, and IFNepitope algorithms were used to identify appropriate epitopes. In our study, we predicted antigenic epitopes of Paracoccidioides that could bind to MHC class II and induce IFN-γ secretion. These T cell epitopes can be used in the development of a laboratory tool to monitor the CMI of patients with PCM.

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Journal articles on the topic 'Basic Local Alignment Search Tool'

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