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Journal articles on the topic 'Consensus sequence'

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Published: 4 June 2021
Last updated: 20 February 2023

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1

Holmes, S. G., and M. M. Smith. "Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain." Molecular and Cellular Biology 9, no. 12 (December 1989): 5464–72. http://dx.doi.org/10.1128/mcb.9.12.5464-5472.1989.

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Yeast autonomously replicating sequence (ARS) elements are composed of a conserved 11-base-pair (bp) core consensus sequence and a less well defined 3'-flanking region. We have investigated the relationship between the H4 ARS core consensus sequence and its 3'-flanking domain. The minimal sequences necessary and sufficient for function were determined by combining external 3' and 5' deletions to produce a nested set of ARS fragments. Sequences 5' of the core consensus were dispensable for function, but at least 66 bp of 3'-flanking domain DNA was required for full ARS function. The importance of the relative orientation of the core consensus element with respect to the 3'-flanking domain was tested by precisely inverting 14 bp of DNA including the core consensus sequence by oligonucleotide mutagenesis. This core inversion mutant was defective for all ARS function, showing that a fixed relative orientation of the core consensus and 3'-flanking domain is required for function. The 3'-flanking domain of the minimal functional H4 ARS fragment contains three sequences with a 9-of-11-bp match to the core consensus. The role of these near-match sequences was tested by directed mutagenesis. When all near-match sequences with an 8-of-11-bp match or better were simultaneously disrupted by point mutations, the resulting ARS construct retained full replication function. Therefore, multiple copies of a sequence closely related to the core consensus element are not required for H4 ARS function.
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2

Holmes, S. G., and M. M. Smith. "Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain." Molecular and Cellular Biology 9, no. 12 (December 1989): 5464–72. http://dx.doi.org/10.1128/mcb.9.12.5464.

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Yeast autonomously replicating sequence (ARS) elements are composed of a conserved 11-base-pair (bp) core consensus sequence and a less well defined 3'-flanking region. We have investigated the relationship between the H4 ARS core consensus sequence and its 3'-flanking domain. The minimal sequences necessary and sufficient for function were determined by combining external 3' and 5' deletions to produce a nested set of ARS fragments. Sequences 5' of the core consensus were dispensable for function, but at least 66 bp of 3'-flanking domain DNA was required for full ARS function. The importance of the relative orientation of the core consensus element with respect to the 3'-flanking domain was tested by precisely inverting 14 bp of DNA including the core consensus sequence by oligonucleotide mutagenesis. This core inversion mutant was defective for all ARS function, showing that a fixed relative orientation of the core consensus and 3'-flanking domain is required for function. The 3'-flanking domain of the minimal functional H4 ARS fragment contains three sequences with a 9-of-11-bp match to the core consensus. The role of these near-match sequences was tested by directed mutagenesis. When all near-match sequences with an 8-of-11-bp match or better were simultaneously disrupted by point mutations, the resulting ARS construct retained full replication function. Therefore, multiple copies of a sequence closely related to the core consensus element are not required for H4 ARS function.
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3

Burke, Kelly, Supriya Munshaw, William Osburn, Jordana Levine, Lin Liu, Stuart Ray, and Andrea Cox. "HCV genotype 1a representative sequence elicits broad CD8+ T cell responses (113.10)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 113.10. http://dx.doi.org/10.4049/jimmunol.188.supp.113.10.

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Abstract Vaccines designed to prevent or to treat hepatitis C viral infection must achieve maximum cross-reactivity against widely divergent circulating strains. Computer-generated sequences minimize genetic distance between circulating strains, and can be generated as a consensus sequence (most common amino acid at each position) or a representative sequence (derived with Bayesian and maximal likelihood phylogenetic tools). Broad recognition of such sequences in HCV has not been demonstrated. Consensus and representative sequences were generated from 390 full-length HCV genotype 1a polypeptide sequences. Sequence mutations in known epitopes were identified by longitudinal sequencing of HCV-infected subjects. Peptides encoding consensus, representative, and variant epitope sequences were tested for the capacity to expand CD8 T cells from HCV-infected subjects and to elicit cross-reactive responses by IFNg ELISpot. The representative and consensus sequences were identical for 9/11 epitopes examined. T cell lines generated against representative sequence peptides were generally cross-reactive to consensus sequence and natural sequence variants. Furthermore, representative sequence peptides generated more robust T cell responses than did natural sequence variant peptides. The broadest recognition of highly diverse circulating HCV strains was achieved using CD8+ T cells expanded with representative sequence HCV. These data support the use of representative sequence in HCV vaccine design.
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4

Du Toit, Andrea. "A consensus pausing sequence." Nature Reviews Microbiology 12, no. 6 (May 16, 2014): 394. http://dx.doi.org/10.1038/nrmicro3286.

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5

Palca, Joseph. "No consensus on sequence." Nature 322, no. 6078 (July 1986): 397. http://dx.doi.org/10.1038/322397a0.

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6

Aitken, Alastair. "Protein Consensus Sequence Motifs." Molecular Biotechnology 12, no. 3 (1999): 241–54. http://dx.doi.org/10.1385/mb:12:3:241.

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7

TORSHIN, Ivan. "Direct and reversed amino acid sequence pattern analysis: structural reasons for activity of reversed sequence sites and results of kinase site mutagenesis." Biochemical Journal 345, no. 3 (January 25, 2000): 733–40. http://dx.doi.org/10.1042/bj3450733.

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During studies of kinase phosphorylation, not all functional kinase phosphorylation may be found using consensus sequence patterns. This type of phosphorylation is termed ‘non-consensus’ or ‘cryptic’ phosphorylation. Results presented here based on molecular dynamics of short peptides show that protein kinases may phosphorylate not only established consensus sequences (reading a sequence from N-terminus to C-terminus) but also reversed consensus sequences (reading from C- to N-terminus). Several protein sequences were analysed and corresponding biochemical data were presented. Similarity of molecular shapes of direct and reversed consensus peptides, and sequence conservation in the regions of reversed sites in the analysed proteins, indicate that at least part of the phosphorylation sites considered as ‘cryptic’ may be explained in terms of reversed consensus pattern occurrences.
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8

Bae, J., U. R. Desai, A. Pervin, E. E. O. Caldwell, J. M. Weiler, and R. J. Linhardt. "Interaction of heparin with synthetic antithrombin III peptide analogues." Biochemical Journal 301, no. 1 (July 1, 1994): 121–29. http://dx.doi.org/10.1042/bj3010121.

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Heparin-binding proteins may contain specific patterns of basic amino acids, called consensus sequences, that interact with heparin. Small peptides were synthesized that contained consensus sequences (i.e. FAKLNCRLYRKANKSSK) or disrupted consensus sequences (i.e. K136-->A) based on the known sequence of antithrombin III (amino acid residues 123-139). These peptides were then examined in both competitive and non-competitive binding experiments using bioassays, fluorescence spectroscopy, affinity chromatography and n.m.r. spectroscopy. Both the consensus and disrupted-consensus peptide bound to heparin. Peptides with consensus sequences bound specifically to the pentasaccharide antithrombin III-binding site within heparin. In contrast, peptides with disrupted consensus sequences showed no specificity, binding to any sequence within heparin. Proton nuclear Overhauser enhancement spectroscopy demonstrated the proximity of leucine and tyrosine (within the consensus sequence) to the N-acetyl moiety found primarily within the pentasaccharide antithrombin III-binding site of heparin. This experiment confirmed the findings of the other techniques and helped to localize the binding sites in both peptides and heparin. A model is proposed for both specific and non-specific heparin interaction with consensus and disrupted-consensus peptides.
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9

Yeh, Ren-Hwa, Tae Ryong Lee, and David S. Lawrence. "From Consensus Sequence Peptide to High Affinity Ligand, a “Library Scan” Strategy." Journal of Biological Chemistry 276, no. 15 (January 16, 2001): 12235–40. http://dx.doi.org/10.1074/jbc.m011232200.

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A wide variety of proteins have been shown to recognize and bind to specific amino acid sequences on other proteins. These sequences can be readily identified using combinatorial peptide libraries. However, peptides containing these preferred sequences (“consensus sequence peptides”) typically display only modest affinities for the consensus sequence-binding site on the intact protein. In this report, we describe a parallel synthesis strategy that transforms consensus sequence peptides into high affinity ligands. The work described herein has focused on the Lck SH2 domain, which binds the consensus peptide acetyl-Tyr(P)-Glu-Glu-Ile-amide with aKDof 1.3 μm. We employed a strategy that creates a series of spatially focused libraries that challenge specific subsites on the target protein with a diverse array of functionality. The final lead compound identified in this study displayed a 3300-fold higher affinity for the Lck SH2 domain than the starting consensus sequence peptide.
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10

Schneider, Thomas D., and R. Michael Stephens. "Sequence logos: a new way to display consensus sequences." Nucleic Acids Research 18, no. 20 (1990): 6097–100. http://dx.doi.org/10.1093/nar/18.20.6097.

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11

Ferrara, P. "Identification of protein consensus sequence." Biochimie 72, no. 12 (December 1990): 898–99. http://dx.doi.org/10.1016/0300-9084(90)90014-8.

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12

Waterman, Michael S. "Multiple sequence alignment by consensus." Nucleic Acids Research 14, no. 22 (1986): 9095–102. http://dx.doi.org/10.1093/nar/14.22.9095.

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13

Nelson, Adin, Ivelise Rijo, Zhigang Zhang, Andrew D. Zelenetz, and Ariela Noy. "Feasiblity and Implication of Bidirectional Sequencing Using a Multiplex Framework 2 Region Primer for Somatic Mutation Analysis of the Immunoglobulin (IgH) Heavy Chain in Chronic Lymphocytic Leukemia (CLL)." Blood 110, no. 11 (November 16, 2007): 4706. http://dx.doi.org/10.1182/blood.v110.11.4706.4706.

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Abstract Background: A somatic mutation rate of >2% of the immunoglobulin (IgH) heavy chain gene, in comparison to germline DNA, is a positive prognostic indicator in chronic lymphocytic leukemia (CLL). Genomic DNA is amplified using the Biomed-2 multiplex PCR primer set, sequenced in the reverse direction only using a 3′ JH primer, and compared to the germline sequence in VBase, a comprehensive directory of all human germline variable region sequences compiled from over a thousand published sequences. It is unknown whether forward sequencing using the multiplex 5′ Biomed-2 primers in a single reaction is feasible or whether doing so improves the accuracy of the mutational analysis. Methods: DNA was extracted from peripheral blood or bone marrow mononuclear cells from patients with CLL using the QIAGEN QIAspin DNA mini-kit. The FR2 region of the IgH gene was amplified using tube B of the Biomed-2 multiplex PCR primer set, separated in 2% agarose gel, excised, and prepared for sequencing using the QIAGEN QIAquick gel extraction kit. Bidirectional DNA sequencing was performed with the full set of multiplex 5′ FR2 primers combined in one reaction for the forward sequence and in a second reaction with the Biomed-2 3′ JH primer for the reverse sequence. A consensus sequence was obtained and mutation rates were calculated based on the consensus sequence and the reverse sequence separately. Results: The FR2 region was amplified from 30 CLL patients. 20 samples produced bidirectional consensus DNA sequences, 2 sequenced only with multiplex FR2 primers, 6 sequenced only with a JH primer, and 2 produced no sequences. Compared with unidirectional JH sequencing, bidirectional sequencing did not reassign any patient in the germline IgH group to the mutated category. In 15 patients, the uni- and bi-directional sequencing were identical. In 4 patients, a single basepair difference was noted. A random permutation test yields a two-sided p-value as 12.5%, indicating that no significant difference was detected between the uni- and bi-directional sequencing. Multiplex bidirectional sequencing did provide sequence information within the CDR3 region at the 3′ terminus of the amplimer which is partially truncated when using the JH primer alone. Conclusion: Bidirectional sequencing does not provide a somatic IgH mutation rate that differs significantly from that obtained from the reverse sequence alone and does not likely influence the IgH mutational prognostic assignment. Nonetheless, the bidirectional consensus sequence adds bases in the CDR3 region which can be used for research applications such as the generation of patient-specific primers for PCR. It is also noteworthy that multiplex PCR using the Biomed-2 primers is feasible.
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14

Mitchell, Michael S., Ellen T. Bodine, Shawn Hill, Gerald Princler, Patricia Lloyd, Hiroaki Mitsuya, Masao Matsuoka, and David Derse. "Phenotypic and Genotypic Comparisons of Human T-Cell Leukemia Virus Type 1 Reverse Transcriptases from Infected T-Cell Lines and Patient Samples." Journal of Virology 81, no. 9 (February 7, 2007): 4422–28. http://dx.doi.org/10.1128/jvi.02660-06.

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ABSTRACT It is well established that cell-free infection with human T-cell leukemia virus type 1 (HTLV-1) is less efficient than that with other retroviruses, though the specific infectivities of only a limited number of HTLV-1 isolates have been quantified. Earlier work indicated that a postentry step in the infectious cycle accounted for the poor cell-free infectivity of HTLV-1. To determine whether variations in the pol gene sequence correlated with virus infectivity, we sequenced and phenotypically tested pol genes from a variety of HTLV-1 isolates derived from primary sources, transformed cell lines, and molecular clones. The pol genes and deduced amino acid sequences from 23 proviruses were sequenced and compared with 14 previously published sequences, revealing a limited number of amino acid variations among isolates. The variations appeared to be randomly dispersed among primary isolates and proviruses from cell lines and molecular clones. In addition, there was no correlation between reverse transcriptase sequence and the disease phenotype of the original source of the virus isolate. HTLV-1 pol gene fragments encoding reverse transcriptase were amplified from a variety of isolates and were subcloned into HTLV-1 vectors for both single-cycle infection and spreading-infection assays. Vectors carrying pol genes that matched the consensus sequence had the highest titers, and those with the largest number of variations from the consensus had the lowest titers. The molecular clone from CS-1 cells had four amino acid differences from the consensus sequence and yielded infectious titers that were approximately eight times lower than those of vectors encoding a consensus reverse transcriptase.
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15

Larkin, J. C., J. R. Thompson, and J. L. Woolford. "Structure and expression of the Saccharomyces cerevisiae CRY1 gene: a highly conserved ribosomal protein gene." Molecular and Cellular Biology 7, no. 5 (May 1987): 1764–75. http://dx.doi.org/10.1128/mcb.7.5.1764-1775.1987.

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The Saccharomyces cerevisiae CRY1 gene encodes ribosomal protein rp59, a component of the 40S ribosomal subunit. Mutations in CRY1 can confer resistance to the alkaloid cryptopleurine, an inhibitor of the elongation step of translation. The nucleotide sequence of the cloned CRY1 gene was determined. The predicted amino acid sequence shows that CRY1 encodes a 14,561-dalton polypeptide that has 88% amino acid sequence homology to the hamster or human S14 ribosomal protein responsible for emetine resistance and 45% homology to Escherichia coli ribosomal protein S11. Analysis of the DNA sequences upstream from CRY1 revealed the presence of three sequences, HOMOL1 (consensus, A/TACATCC/TG/ATA/GCA), RPG (consensus, ACCCA/GTACATT/CT/A), and a thymine-rich sequence, found upstream of more than 20 other cloned yeast genes encoding components of the translational apparatus. We exploited the ability to assay the expression of CRY1 in vivo by using the cryptopleurine resistance phenotype to demonstrate that these three consensus sequences are necessary for the transcription of CRY1. We previously showed that the upstream promoter element of the yeast RP39A gene consists of these identical sequence motifs. Therefore, we suggest that these three sequences define a consensus promoter element for the genes encoding the yeast translational apparatus. CRY1 is one of several hundred yeast genes, including ribosomal protein genes, whose expression is transiently decreased 10-fold upon heat shock. We found that the HOMOL1 and RPG consensus sequences are not necessary for the heat shock response of CRY1.
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16

Larkin, J. C., J. R. Thompson, and J. L. Woolford. "Structure and expression of the Saccharomyces cerevisiae CRY1 gene: a highly conserved ribosomal protein gene." Molecular and Cellular Biology 7, no. 5 (May 1987): 1764–75. http://dx.doi.org/10.1128/mcb.7.5.1764.

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The Saccharomyces cerevisiae CRY1 gene encodes ribosomal protein rp59, a component of the 40S ribosomal subunit. Mutations in CRY1 can confer resistance to the alkaloid cryptopleurine, an inhibitor of the elongation step of translation. The nucleotide sequence of the cloned CRY1 gene was determined. The predicted amino acid sequence shows that CRY1 encodes a 14,561-dalton polypeptide that has 88% amino acid sequence homology to the hamster or human S14 ribosomal protein responsible for emetine resistance and 45% homology to Escherichia coli ribosomal protein S11. Analysis of the DNA sequences upstream from CRY1 revealed the presence of three sequences, HOMOL1 (consensus, A/TACATCC/TG/ATA/GCA), RPG (consensus, ACCCA/GTACATT/CT/A), and a thymine-rich sequence, found upstream of more than 20 other cloned yeast genes encoding components of the translational apparatus. We exploited the ability to assay the expression of CRY1 in vivo by using the cryptopleurine resistance phenotype to demonstrate that these three consensus sequences are necessary for the transcription of CRY1. We previously showed that the upstream promoter element of the yeast RP39A gene consists of these identical sequence motifs. Therefore, we suggest that these three sequences define a consensus promoter element for the genes encoding the yeast translational apparatus. CRY1 is one of several hundred yeast genes, including ribosomal protein genes, whose expression is transiently decreased 10-fold upon heat shock. We found that the HOMOL1 and RPG consensus sequences are not necessary for the heat shock response of CRY1.
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17

Makino, S., and M. Joo. "Effect of intergenic consensus sequence flanking sequences on coronavirus transcription." Journal of Virology 67, no. 6 (1993): 3304–11. http://dx.doi.org/10.1128/jvi.67.6.3304-3311.1993.

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18

Lee, C. "Generating consensus sequences from partial order multiple sequence alignment graphs." Bioinformatics 19, no. 8 (May 22, 2003): 999–1008. http://dx.doi.org/10.1093/bioinformatics/btg109.

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19

JEONG, YONG SEOK, JOHN F. REPASS, YOUNG-NAM KIM, SUN-MIN HWANG, and SHINJI MAKINO. "Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence." Virology 217, no. 1 (March 1996): 311–22. http://dx.doi.org/10.1006/viro.1996.0118.

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20

Gibson, Keylie M., Margaret C. Steiner, Uzma Rentia, Matthew L. Bendall, Marcos Pérez-Losada, and Keith A. Crandall. "Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses." Viruses 12, no. 7 (July 14, 2020): 758. http://dx.doi.org/10.3390/v12070758.

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Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.
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21

Collatz, Maximilian, Sascha D. Braun, Stefan Monecke, and Ralf Ehricht. "ConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design." BioMedInformatics 2, no. 4 (November 24, 2022): 637–42. http://dx.doi.org/10.3390/biomedinformatics2040041.

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Background: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated. Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays. Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.
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22

Spirollari, Junilda, Jason T. L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park, and Bruce A. Shapiro. "Predicting Consensus Structures for RNA Alignments via Pseudo-Energy Minimization." Bioinformatics and Biology Insights 3 (January 2009): BBI.S2578. http://dx.doi.org/10.4137/bbi.s2578.

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Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results from these algorithms are promising, an observation is that single sequence-based methods have moderate accuracy and more information is needed to improve on RNA secondary structure prediction, such as covariance scores obtained from multiple sequence alignments. We present in this paper a new approach to predicting the consensus secondary structure of a set of aligned RNA sequences via pseudo-energy minimization. Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement. RSpredict accepts, as input data, a multiple sequence alignment in FASTA or ClustalW format and outputs the consensus secondary structure of the input sequences in both the Vienna style Dot Bracket format and the Connectivity Table format. Our method was compared with some widely used tools including KNetFold, Pfold and RNAalifold. A comprehensive test on different datasets including Rfam sequence alignments and a multiple sequence alignment obtained from our study on the Drosophila X chromosome reveals that RSpredict is competitive with the existing tools on the tested datasets. RSpredict is freely available online as a web server and also as a jar file for download at http://datalab.njit.edu/biology/RSpredict .
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23

White, Kris, Hua Peng, John Hay, and William T. Ruyechan. "Role of the IE62 Consensus Binding Site in Transactivation by the Varicella-Zoster Virus IE62 Protein." Journal of Virology 84, no. 8 (February 3, 2010): 3767–79. http://dx.doi.org/10.1128/jvi.02522-09.

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ABSTRACT The varicella-zoster virus (VZV) IE62 protein is the major transcriptional activator. IE62 is capable of associating with DNA both nonspecifically and in a sequence-specific manner via a consensus binding site (5′-ATCGT-3′). However, the function of the consensus site is poorly understood, since IE62 efficiently transactivates promoter elements lacking this sequence. In the work presented here, sequence analysis of the VZV genome revealed the presence of 245 IE62 consensus sites throughout the genome. Some 54 sites were found to be present within putative VZV promoters. Electrophoretic mobility shift assay (EMSA) experiments using an IE62 fragment containing the IE62 DNA-binding domain and duplex oligonucleotides that did or did not contain the IE62 consensus binding sequence yielded KD (equilibrium dissociation constant) values in the nanomolar range. Further, the IE62 DNA binding domain was shown to have a 5-fold-increased affinity for its consensus site compared to nonconsensus sequences. The effect of consensus site presence and position on IE62-mediated activation of native VZV and model promoters was examined using site-specific mutagenesis and transfection and superinfection reporter assays. In all promoters examined, the consensus sequence functioned as a distance-dependent repressive element. Protein recruitment assays utilizing the VZV gI promoter indicated that the presence of the consensus site increased the recruitment of IE62 but not Sp1. These data suggest a model where the IE62 consensus site functions to down-modulate IE62 activation, and interaction of IE62 with this sequence may result in loss or decrease of the ability of IE62 to recruit cellular factors needed for full promoter activation.
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24

Arredondo-Peter, R., and E. Escamilla. "A consensus sequence of plant hemoglobins." Plant Molecular Biology Reporter 9, no. 3 (August 1991): 195–207. http://dx.doi.org/10.1007/bf02672068.

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25

Heraclides, Alexandros, and Eva Fernández-Domínguez. "Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods." International Journal of Molecular Sciences 23, no. 9 (April 22, 2022): 4651. http://dx.doi.org/10.3390/ijms23094651.

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Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.
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26

Hiszczyńska-Sawicka, E., and J. Kur. "Binding of Escherichia coli integration host factor (IHF) to the origin segment of p15A plasmid." Acta Biochimica Polonica 42, no. 1 (March 31, 1995): 103–8. http://dx.doi.org/10.18388/abp.1995_4675.

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The integration host factor (IHF) is a sequence-specific, histone-like, multi-functional DNA-binding and -bending protein of Escherichia coli. Characterization and functional analysis of this protein has been carried out mainly in bacteriophage lambda and other mobile genetic elements. In this paper we report data concerning the binding of IHF protein to the plasmid orip15A region. IHF binds to the single site of the DNA fragment containing the orip15A, as shown by the gel mobility shift assays and footprinting experiment. On the basis of the ihf consensus sequences published, we have been able to identify one sequence of putative ihf site into the orip15A sequence with two mismatches in relation to the consensus sequence of Kur et al., 1989, Gene 81, 1-15. One ihf binding site was also found in the oriColE1 region sequence with three mismatches in relation to this consensus sequence.
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27

Sun, Hanzhen, and Lawrence A. Chasin. "Multiple Splicing Defects in an Intronic False Exon." Molecular and Cellular Biology 20, no. 17 (September 1, 2000): 6414–25. http://dx.doi.org/10.1128/mcb.20.17.6414-6425.2000.

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ABSTRACT Splice site consensus sequences alone are insufficient to dictate the recognition of real constitutive splice sites within the typically large transcripts of higher eukaryotes, and large numbers of pseudoexons flanked by pseudosplice sites with good matches to the consensus sequences can be easily designated. In an attempt to identify elements that prevent pseudoexon splicing, we have systematically altered known splicing signals, as well as immediately adjacent flanking sequences, of an arbitrarily chosen pseudoexon from intron 1 of the human hprt gene. The substitution of a 5′ splice site that perfectly matches the 5′ consensus combined with mutation to match the CAG/G sequence of the 3′ consensus failed to get this model pseudoexon included as the central exon in a dhfr minigene context. Provision of a real 3′ splice site and a consensus 5′ splice site and removal of an upstream inhibitory sequence were necessary and sufficient to confer splicing on the pseudoexon. This activated context also supported the splicing of a second pseudoexon sequence containing no apparent enhancer. Thus, both the 5′ splice site sequence and the polypyrimidine tract of the pseudoexon are defective despite their good agreement with the consensus. On the other hand, the pseudoexon body did not exert a negative influence on splicing. The introduction into the pseudoexon of a sequence selected for binding to ASF/SF2 or its replacement with β-globin exon 2 only partially reversed the effect of the upstream negative element and the defective polypyrimidine tract. These results support the idea that exon-bridging enhancers are not a prerequisite for constitutive exon definition and suggest that intrinsically defective splice sites and negative elements play important roles in distinguishing the real splicing signal from the vast number of false splicing signals.
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Kikuchi, Hideaki, Takao Sekiya, Susumu Nishimura, and Minro Watanabe. "Rat repetitive sequence: consensus sequence ofTag1–298 base pairs fragment." Nucleic Acids Research 15, no. 19 (1987): 8107–8. http://dx.doi.org/10.1093/nar/15.19.8107.

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29

Fyfe, Janet A. M., and John K. Davies. "An AT-Rich Tract Containing an Integration Host Factor-Binding Domain and Two UP-Like Elements Enhances Transcription from thepilEp1 Promoter of Neisseria gonorrhoeae." Journal of Bacteriology 180, no. 8 (April 15, 1998): 2152–59. http://dx.doi.org/10.1128/jb.180.8.2152-2159.1998.

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ABSTRACT The pilE gene of Neisseria gonorrhoeae is transcribed from a ς70 promoter (pilEp 1) with an AT-rich tract extending 65 nucleotides upstream of the −35 box. Within this region is an integration host factor (IHF)-binding core consensus sequence. We have performed a detailed analysis to determine which upstream sequences are required for efficient transcription frompilEp 1 in N. gonorrhoeae. Deletion of sequences upstream of the AT-rich tract had no effect on the level of transcription. However, the IHF-binding core consensus sequence and the AT-rich sequence further upstream were both required for enhanced levels of transcription from this promoter in both N. gonorrhoeae and an Escherichia coli strain producing IHF. In addition, an UP-like element positioned between the −35 box and the IHF-binding site was required for maximal transcription. The AT-rich region upstream of the IHF-binding core consensus sequence can also act as an UP-like element when appropriately repositioned upstream of the −35 box.
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Doree, Scott M., and Martha H. Mulks. "Identification of an Actinobacillus pleuropneumoniae Consensus Promoter Structure." Journal of Bacteriology 183, no. 6 (March 15, 2001): 1983–89. http://dx.doi.org/10.1128/jb.183.6.1983-1989.2001.

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ABSTRACT Actinobacillus pleuropneumoniaepromoter-containing clones were isolated from a genomic DNA library constructed in our lVET promoter trap vector pTF86. The promoter-containing clones were identified by their ability to drive expression of the promoterless luxAB genes of Vibrio harveyi. The degree of expression was quantifiable, and only high-expression or “hot” promoters were used for this study. Nine clones were sequenced, and their transcriptional start sites were determined by primer extension. The sequences upstream of the start site were aligned, and a consensus promoter structure for A. pleuropneumoniae was identified. The consensus promoter sequence for A. pleuropneumoniae was found to be TATAAT and TTG/AAA, centered approximately 10 and 35 bp upstream of the transcriptional start site, respectively. A comparison of the A. pleuropneumoniae consensus with other prokaryotic consensus promoters showed that the A. pleuropneumoniaeconsensus promoter is similar to that found in other eubacteria in terms of sequence, with an identical −10 element and a similar but truncated −35 element. However, the A. pleuropneumoniaeconsensus promoter is unique in the spacing between the −10 and −35 elements. The promoter spacing was analyzed by site-directed mutagenesis, which demonstrated that optimal spacing for an A. pleuropneumoniae promoter is shorter than the spacing identified for Escherichia coli and Bacillus subtilispromoters.
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Kociumaka, Tomasz, Jakub W. Pachocki, Jakub Radoszewski, Wojciech Rytter, and Tomasz Waleń. "On the string consensus problem and the Manhattan sequence consensus problem." Theoretical Computer Science 710 (February 2018): 126–38. http://dx.doi.org/10.1016/j.tcs.2017.03.022.

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32

Sternke, Matt, Katherine W. Tripp, and Doug Barrick. "Consensus sequence design as a general strategy to create hyperstable, biologically active proteins." Proceedings of the National Academy of Sciences 116, no. 23 (May 20, 2019): 11275–84. http://dx.doi.org/10.1073/pnas.1816707116.

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Consensus sequence design offers a promising strategy for designing proteins of high stability while retaining biological activity since it draws upon an evolutionary history in which residues important for both stability and function are likely to be conserved. Although there have been several reports of successful consensus design of individual targets, it is unclear from these anecdotal studies how often this approach succeeds and how often it fails. Here, we attempt to assess generality by designing consensus sequences for a set of six protein families with a range of chain lengths, structures, and activities. We characterize the resulting consensus proteins for stability, structure, and biological activities in an unbiased way. We find that all six consensus proteins adopt cooperatively folded structures in solution. Strikingly, four of six of these consensus proteins show increased thermodynamic stability over naturally occurring homologs. Each consensus protein tested for function maintained at least partial biological activity. Although peptide binding affinity by a consensus-designed SH3 is rather low, Km values for consensus enzymes are similar to values from extant homologs. Although consensus enzymes are slower than extant homologs at low temperature, they are faster than some thermophilic enzymes at high temperature. An analysis of sequence properties shows consensus proteins to be enriched in charged residues, and rarified in uncharged polar residues. Sequence differences between consensus and extant homologs are predominantly located at weakly conserved surface residues, highlighting the importance of these residues in the success of the consensus strategy.
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Christlet, T. Hema Thanka, M. Biswas, and K. Veluraja. "A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences." Acta Crystallographica Section D Biological Crystallography 55, no. 8 (August 1, 1999): 1414–20. http://dx.doi.org/10.1107/s0907444999006010.

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An analysis of the frequency of occurrence of various residues at position X was carried out on the consensus glycosylating sequence Asn-X-Ser/Thr using the PDB three-dimensional database. 488 non-homologous proteins bearing 696 Asn-X-Ser/Thr (X ≠ Pro) sequences were analysed. More than 65% of Asn residues, when they occur as part of the consensus sequence, lie on the surface of the protein, implying a potentiality for glycosylation. A deviation parameter (DP) was calculated as a measure of preferential (positive) or non-preferential (negative) selection. At the X position in the consensus-sequence segment, the amino acids Gly, Asn and Phe have statistically significant positive DP values. The high value of DP for Asn is a consequence of the preferential occurrence of homodoublets, while for Phe it may be a consequence of the stacking interaction of the aromatic ring with the glycan. Gly at the X position in the consensus glycosylating sequence may be functionally significant owing to its preference and its high percentage of occurrence in proteins. The Ramachandran (Φ,Ψ) angles around Gly in the consensus sequence show clustering in the region which is disallowed for non-glycyl residues. In this region, a hydrogen bond between the side chain of Asn and the peptide backbone/side chain of Ser/Thr is possible, reflecting a positional as well as a conformational role in the consensus glycosylating sequence. For the 44 confirmed N-glycosylating sequences, an in-depth analysis of the (Ψ N , Φ X , Ψ X , Φ S/T ) dihedral angles, which position the side chains of Asn and Ser/Thr, shows that these can be grouped into nine conformational states. In most cases, a direct or water-mediated hydrogen bond between OD1 of Asn and OG of Ser/Thr is possible, reflecting the possible importance of this hydrogen bonding in the glycosylation process.
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Miller, C. A., and D. Kowalski. "cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 9 (September 1993): 5360–69. http://dx.doi.org/10.1128/mcb.13.9.5360-5369.1993.

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The ribosomal DNA (rDNA) repeats of Saccharomyces cerevisiae contain an autonomously replicating sequence (ARS) that colocalizes with a chromosomal origin of replication. We show that a minimal sequence necessary for full ARS function corresponds to a 107-bp rDNA fragment which contains three 10-of-11-bp matches to the ARS consensus sequence. Point mutations in only one of the 10-of-11-bp matches, GTTTAT GTTTT, inactivate the rDNA ARS, indicating that this consensus sequence is essential. A perfect match to a revised ARS consensus is present but not essential. Sequences up to 9 bp 5' from the essential consensus are dispensable. A broad DNA region directly 3' to the essential consensus is required and is easily unwound as indicated by: (i) hypersensitivity to nicking of an approximately 100-bp region by mung bean nuclease in a negatively supercoiled plasmid and (ii) helical instability determined by thermodynamic analysis of the nucleotide sequence. A correlation between DNA helical instability and replication efficiency of wild-type and mutated ribosomal ARS derivatives suggests that a broad region 3' to the essential ARS consensus functions as a DNA unwinding element. Certain point mutations that do not stabilize the DNA helix in the 3' region but reduce ARS efficiency reveal an element distinct from, but overlapping, the DNA unwinding element. The nucleotide sequence of the functionally important constituents in the ARS appears to be conserved among the rDNA repeats in the chromosome.
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Miller, C. A., and D. Kowalski. "cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 9 (September 1993): 5360–69. http://dx.doi.org/10.1128/mcb.13.9.5360.

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The ribosomal DNA (rDNA) repeats of Saccharomyces cerevisiae contain an autonomously replicating sequence (ARS) that colocalizes with a chromosomal origin of replication. We show that a minimal sequence necessary for full ARS function corresponds to a 107-bp rDNA fragment which contains three 10-of-11-bp matches to the ARS consensus sequence. Point mutations in only one of the 10-of-11-bp matches, GTTTAT GTTTT, inactivate the rDNA ARS, indicating that this consensus sequence is essential. A perfect match to a revised ARS consensus is present but not essential. Sequences up to 9 bp 5' from the essential consensus are dispensable. A broad DNA region directly 3' to the essential consensus is required and is easily unwound as indicated by: (i) hypersensitivity to nicking of an approximately 100-bp region by mung bean nuclease in a negatively supercoiled plasmid and (ii) helical instability determined by thermodynamic analysis of the nucleotide sequence. A correlation between DNA helical instability and replication efficiency of wild-type and mutated ribosomal ARS derivatives suggests that a broad region 3' to the essential ARS consensus functions as a DNA unwinding element. Certain point mutations that do not stabilize the DNA helix in the 3' region but reduce ARS efficiency reveal an element distinct from, but overlapping, the DNA unwinding element. The nucleotide sequence of the functionally important constituents in the ARS appears to be conserved among the rDNA repeats in the chromosome.
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36

Xu, Jian, Barbara C. McCabe, and Gerald B. Koudelka. "Function-Based Selection and Characterization of Base-Pair Polymorphisms in a Promoter of Escherichia coli RNA Polymerase-ς70." Journal of Bacteriology 183, no. 9 (May 1, 2001): 2866–73. http://dx.doi.org/10.1128/jb.183.9.2866-2873.2001.

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ABSTRACT We performed two sets of in vitro selections to dissect the role of the −10 base sequence in determining the rate and efficiency with which Escherichia coli RNA polymerase-ς70forms stable complexes with a promoter. We identified sequences that (i) rapidly form heparin-resistant complexes with RNA polymerase or (ii) form heparin-resistant complexes at very low RNA polymerase concentrations. The sequences selected under the two conditions differ from each other and from the consensus −10 sequence. The selected promoters have the expected enhanced binding and kinetic properties and are functionally better than the consensus promoter sequence in directing RNA synthesis in vitro. Detailed analysis of the selected promoter functions shows that each step in this multistep pathway may have different sequence requirements, meaning that the sequence of a strong promoter does not contain the optimal sequence for each step but instead is a compromise sequence that allows all steps to proceed with minimal constraint.
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37

Ray, Stuart C., Liam Fanning, Xiao-Hong Wang, Dale M. Netski, Elizabeth Kenny-Walsh, and David L. Thomas. "Divergent and convergent evolution after a common-source outbreak of hepatitis C virus." Journal of Experimental Medicine 201, no. 11 (June 6, 2005): 1753–59. http://dx.doi.org/10.1084/jem.20050122.

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The genomic sequences of viruses that are highly mutable and cause chronic infection tend to diverge over time. We report that these changes represent both immune-driven selection and, in the absence of immune pressure, reversion toward an ancestral consensus. Sequence changes in hepatitis C virus (HCV) structural and nonstructural genes were studied in a cohort of women accidentally infected with HCV in a rare common-source outbreak. We compared sequences present in serum obtained 18–22 yr after infection to sequences present in the shared inoculum and found that HCV evolved along a distinct path in each woman. Amino acid substitutions in known epitopes were directed away from consensus in persons having the HLA allele associated with that epitope (immune selection), and toward consensus in those lacking the allele (reversion). These data suggest that vaccines for genetically diverse viruses may be more effective if they represent consensus sequence, rather than a human isolate.
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38

Van Houten, J. V., and C. S. Newlon. "Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III." Molecular and Cellular Biology 10, no. 8 (August 1990): 3917–25. http://dx.doi.org/10.1128/mcb.10.8.3917-3925.1990.

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Yeast autonomously replicating sequence (ARS) elements contain an 11-base-pair core consensus sequence (5'-[A/T]TTTAT[A/G]TTT[A/T]-3') that is required for function. The contribution of each position within this sequence to ARS activity was tested by creating all possible single-base mutations within the core consensus sequence of ARS307 (formerly called the C2G1 ARS) and testing their effects on high-frequency transformation and on plasmid stability. Of the 33 mutations, 22 abolished ARS function as measured by high-frequency transformation, 7 caused more than twofold reductions in plasmid stability, and 4 had no effect on plasmid stability. Mutations that reduced or abolished ARS activity occurred at each position in the consensus sequence, demonstrating that each position of this sequence contributes to ARS function. Of the four mutations that had no effect on ARS activity, three created alternative perfect matches to the core consensus sequence, demonstrating that the alternate bases allowed by the consensus sequence are, indeed, interchangeable. In addition, a change from T to C at position 6 did not perturb wild-type efficiency. To test whether the essential region extends beyond the 11-base-pair consensus sequence, the effects on plasmid stability of point mutations one base 3' to the T-rich strand of the core consensus sequence (position 12) and deletion mutations that altered bases 5' to the T-rich strand of the core consensus sequence were examined. An A at position 12 or the removal of three T residues 5' to the core consensus sequence severely diminished ARS efficiency, showing that the region required for full ARS efficiency extends beyond the core consensus sequence in both directions.
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39

Van Houten, J. V., and C. S. Newlon. "Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III." Molecular and Cellular Biology 10, no. 8 (August 1990): 3917–25. http://dx.doi.org/10.1128/mcb.10.8.3917.

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Yeast autonomously replicating sequence (ARS) elements contain an 11-base-pair core consensus sequence (5'-[A/T]TTTAT[A/G]TTT[A/T]-3') that is required for function. The contribution of each position within this sequence to ARS activity was tested by creating all possible single-base mutations within the core consensus sequence of ARS307 (formerly called the C2G1 ARS) and testing their effects on high-frequency transformation and on plasmid stability. Of the 33 mutations, 22 abolished ARS function as measured by high-frequency transformation, 7 caused more than twofold reductions in plasmid stability, and 4 had no effect on plasmid stability. Mutations that reduced or abolished ARS activity occurred at each position in the consensus sequence, demonstrating that each position of this sequence contributes to ARS function. Of the four mutations that had no effect on ARS activity, three created alternative perfect matches to the core consensus sequence, demonstrating that the alternate bases allowed by the consensus sequence are, indeed, interchangeable. In addition, a change from T to C at position 6 did not perturb wild-type efficiency. To test whether the essential region extends beyond the 11-base-pair consensus sequence, the effects on plasmid stability of point mutations one base 3' to the T-rich strand of the core consensus sequence (position 12) and deletion mutations that altered bases 5' to the T-rich strand of the core consensus sequence were examined. An A at position 12 or the removal of three T residues 5' to the core consensus sequence severely diminished ARS efficiency, showing that the region required for full ARS efficiency extends beyond the core consensus sequence in both directions.
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40

Castagnone-Sereno, Philippe, Frédéric Leroy, and Pierre Abad. "Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria." Genome 43, no. 2 (March 15, 2000): 346–53. http://dx.doi.org/10.1139/g00-007.

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A new satellite DNA family, named pMaE, has been cloned from the genome of the phytoparasitic nematode, Meloidogyne arenaria (Nematoda: Tylenchida). It is represented as tandemly repeated sequences with a monomeric unit of 172 bp. The monomers are present at approximately 15 700 copies per haploid genome, and represent about 5.3% of the total genomic DNA. Twenty-seven independent monomers have been cloned and sequenced. The deduced consensus sequence is 70.9% A + T rich, with frequent stretches of A and (or) T. Several direct or inverted sub-repeats are present in the sequence, which may allow the formation of a dyad structure, suggesting some potential role of this repetitive sequence in heterochromatin condensation. The monomers are very homogeneous in sequence, showing on average 1.8% divergence from their consensus sequence. Moreover, Southern blot experiments and sequence analysis of homologous monomers from the genome of geographically distinct M. arenaria populations have shown that this satellite DNA is uniformly distributed and highly conserved within the species. Therefore, it is hypothesized that this unusually low level of variability, either within the genome of a given population or between populations, could be achieved as the result of some highly effective homogenization mechanism acting upon the nematode genome. Key words: genomic organization, Meloidogyne arenaria, satellite DNA.
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41

Gültekin, Visam, and Jens Allmer. "Novel perspectives for SARS-CoV-2 genome browsing." Journal of Integrative Bioinformatics 18, no. 1 (March 1, 2021): 19–26. http://dx.doi.org/10.1515/jib-2021-0001.

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Abstract SARS-CoV-2 has spread worldwide and caused social, economic, and health turmoil. The first genome assembly of SARS-CoV-2 was produced in Wuhan, and it is widely used as a reference. Subsequently, more than a hundred additional SARS-CoV-2 genomes have been sequenced. While the genomes appear to be mostly identical, there are variations. Therefore, an alignment of all available genomes and the derived consensus sequence could be used as a reference, better serving the science community. Variations are significant, but representing them in a genome browser can become, especially if their sequences are largely identical. Here we summarize the variation in one track. Other information not currently found in genome browsers for SARS-CoV-2, such as predicted miRNAs and predicted TRS as well as secondary structure information, were also added as tracks to the consensus genome. We believe that a genome browser based on the consensus sequence is better suited when considering worldwide effects and can become a valuable resource in the combating of COVID-19. The genome browser is available at http://cov.iaba.online.
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42

Jamkhedkar, Suruchi. "Characterization of the hypothetical proteins of Human Papillomavirus DNA consensus sequence." Research Journal of Biotechnology 16, no. 7 (June 25, 2021): 197–202. http://dx.doi.org/10.25303/167rjbt19721.

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The diagnosis of HPV infection is generally carried out using immunological and molecular techniques based on high risk to probable high-risk HPV strains. The aim of this work is to generate a global representation of HPV strains for diagnosis and drug development. In this work, all the complete genomic DNA sequences of registered Human Papillomavirus (HPV) strains available in NCBI GenBank were used to obtain a consensus sequence of HPV using the Genetic Algorithm. The consensus DNA sequence was translated using the ExPASy software tool. In all, six longest amino acids frames were selected from the six translated frames. The amino acid sequence identity was carried out using the BLAST tool. The six amino acid sequences were identified as E1, E2, E6, E7, L1 and L2. The homology modeling method (Modeller Software Tool) was used to determine the secondary structure of these six identified primary amino acid sequence. The percentage of similarity ranged from 24% in L2 to 100% in E7 and L1. The functions of these structural domains were also determined from PDB databank, InterProScan and CATH. Hence the consensus sequence built using a genetic algorithm is representative of the HPV genome which can be used for diagnostics and drug development purposes.
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Wang, Mengchi, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, and Wei Wang. "Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss." Genetics 216, no. 2 (August 19, 2020): 353–58. http://dx.doi.org/10.1534/genetics.120.303597.

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Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus sequences. We name this representation as sequence Motto and have implemented an efficient algorithm with flexible options for converting motif PWMs into Motto from nucleotides, amino acids, and customized characters. We show that this representation provides a simple and efficient way to identify the binding sites of 1156 common transcription factors (TFs) in the human genome. The effectiveness of the method was benchmarked by comparing sequence matches found by Motto with PWM scanning results found by FIMO. On average, our method achieves a 0.81 area under the precision-recall curve, significantly (P-value < 0.01) outperforming all existing methods, including maximal positional weight, Cavener’s method, and minimal mean square error. We believe this representation provides a distilled summary of a motif, as well as the statistical justification.
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44

Baig, Tayyba T., Jean-Marc Lanchy, and J. Stephen Lodmell. "Randomization and In Vivo Selection Reveal a GGRG Motif Essential for Packaging Human Immunodeficiency Virus Type 2 RNA." Journal of Virology 83, no. 2 (October 29, 2008): 802–10. http://dx.doi.org/10.1128/jvi.01521-08.

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ABSTRACT The packaging signal (ψ) of human immunodeficiency virus type 2 (HIV-2) is present in the 5′ noncoding region of RNA and contains a 10-nucleotide palindrome (pal; 5′-392-GGAGUGCUCC) located upstream of the dimerization signal stem-loop 1 (SL1). pal has been shown to be functionally important in vitro and in vivo. We previously showed that the 3′ side of pal (GCUCC-3′) is involved in base-pairing interactions with a sequence downstream of SL1 to make an extended SL1, which is important for replication in vivo and the regulation of dimerization in vitro. However, the role of the 5′ side of pal (5′-GGAGU) was less clear. Here, we characterized this role using an in vivo SELEX approach. We produced a population of HIV-2 DNA genomes with random sequences within the 5′ side of pal and transfected these into COS-7 cells. Viruses from COS-7 cells were used to infect C8166 permissive cells. After several weeks of serial passage in C8166 cells, surviving viruses were sequenced. On the 5′ side of pal there was a striking convergence toward a GGRGN consensus sequence. Individual clones with consensus and nonconsensus sequences were tested in infectivity and packaging assays. Analysis of individuals that diverged from the consensus sequence showed normal viral RNA and protein synthesis but had replication defects and impaired RNA packaging. These findings clearly indicate that the GGRG motif is essential for viral replication and genomic RNA packaging.
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45

Edworthy, Nicole L., and Andrew J. Easton. "Mutational analysis of the avian pneumovirus conserved transcriptional gene start sequence identifying critical residues." Journal of General Virology 86, no. 12 (December 1, 2005): 3343–47. http://dx.doi.org/10.1099/vir.0.81352-0.

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Seven of the eight genes in the avian pneumovirus (APV) genome contain a conserved 9 nt transcriptional start sequence with the virus large (L) polymerase gene differing from the consensus at three positions. The sequence requirements of the APV transcriptional gene start sequence were investigated by generating a series of mutations in which each of the nine conserved bases was mutated to each of the other three possible nucleotides in a minigenome containing two reporter genes. The effect of each mutation was assessed by measuring the relative levels of expression from the altered and unaltered gene start sequences. Mutations at positions 2, 7 and 9 significantly reduced transcription levels while alterations to position 5 had little effect. The L gene start sequence directed transcription at levels approximately 50 % below that of the consensus gene start sequence. These data suggest that there are common features in pneumovirus transcriptional control sequences.
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46

Gao, Kaiping, Akio Masuda, Tohru Matsuura, and Kinji Ohno. "Human branch point consensus sequence is yUnAy." Nucleic Acids Research 36, no. 7 (February 19, 2008): 2257–67. http://dx.doi.org/10.1093/nar/gkn073.

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47

Christoffels, A. "STACK: Sequence Tag Alignment and Consensus Knowledgebase." Nucleic Acids Research 29, no. 1 (January 1, 2001): 234–38. http://dx.doi.org/10.1093/nar/29.1.234.

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48

Lo, Kiersten, and Stephen T. Smale. "Generality of a functional initiator consensus sequence." Gene 182, no. 1-2 (December 1996): 13–22. http://dx.doi.org/10.1016/s0378-1119(96)00438-6.

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49

Charlesworth, M., and K. El‐Boghdadly. "Time for consensus on rapid sequence intubation?" Anaesthesia 75, no. 3 (March 2020): 298–300. http://dx.doi.org/10.1111/anae.14906.

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50

Mosquera, C., R. Lopez-Valcarce, and S. K. Jayaweera. "Stepsize Sequence Design for Distributed Average Consensus." IEEE Signal Processing Letters 17, no. 2 (February 2010): 169–72. http://dx.doi.org/10.1109/lsp.2009.2035373.

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