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Journal articles on the topic 'Consensus sequence'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Burke, Kelly, Supriya Munshaw, William Osburn, et al. "HCV genotype 1a representative sequence elicits broad CD8+ T cell responses (113.10)." Journal of Immunology 188, no. 1_Supplement (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 polypeptid

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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 (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

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3

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 (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

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4

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 (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

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5

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 (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 mo

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6

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 (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 cons

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7

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

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8

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

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9

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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10

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 (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 sin

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11

Mitchell, Michael S., Ellen T. Bodine, Shawn Hill, et al. "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 (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

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12

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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13

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 (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

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14

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 (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

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15

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 (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

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16

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

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17

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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18

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 (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. Electrophoreti

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19

Collatz, Maximilian, Sascha D. Braun, Stefan Monecke, and Ralf Ehricht. "ConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design." BioMedInformatics 2, no. 4 (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 seq

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20

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-ene

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21

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 (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 p

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22

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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23

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

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24

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 (1996): 311–22. http://dx.doi.org/10.1006/viro.1996.0118.

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25

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 (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 abl

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26

Sun, Hanzhen, and Lawrence A. Chasin. "Multiple Splicing Defects in an Intronic False Exon." Molecular and Cellular Biology 20, no. 17 (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′ splic

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27

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 (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 r

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28

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 (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-seq

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29

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 (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

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30

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 (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

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31

Xu, Jian, Barbara C. McCabe та 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, № 9 (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 f

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32

Doree, Scott M., and Martha H. Mulks. "Identification of an Actinobacillus pleuropneumoniae Consensus Promoter Structure." Journal of Bacteriology 183, no. 6 (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

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33

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 (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, struct

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34

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 (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

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35

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 (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

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Gültekin, Visam, and Jens Allmer. "Novel perspectives for SARS-CoV-2 genome browsing." Journal of Integrative Bioinformatics 18, no. 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

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37

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 (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 st

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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 (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 st

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39

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 (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

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40

Jamkhedkar, Suruchi. "Characterization of the hypothetical proteins of Human Papillomavirus DNA consensus sequence." Research Journal of Biotechnology 16, no. 7 (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 fr

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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 (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 unalte

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

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Perez, Eduardo, Haiyan Zheng, and Ann M. Stock. "Identification of Methylation Sites in Thermotoga maritima Chemotaxis Receptors." Journal of Bacteriology 188, no. 11 (2006): 4093–100. http://dx.doi.org/10.1128/jb.00181-06.

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ABSTRACT Adaptation in bacterial chemotaxis involves reversible methylation of specific glutamate residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins. The specific sites of methylation in Salmonella enterica and Escherichia coli chemoreceptors, identified 2 decades ago, established a consensus sequence for methylation by methyltransferase CheR. Here we report the in vitro methylation of chemoreceptors from Thermotoga maritima, a hyperthermophile that has served as a useful source of chemotaxis proteins for structural analysis. Sites of methylation have been identifi

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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 (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 seque

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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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Dubreuil, R. R., T. J. Byers, A. L. Sillman, D. Bar-Zvi, L. S. Goldstein, and D. Branton. "The complete sequence of Drosophila alpha-spectrin: conservation of structural domains between alpha-spectrins and alpha-actinin." Journal of Cell Biology 109, no. 5 (1989): 2197–205. http://dx.doi.org/10.1083/jcb.109.5.2197.

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We report the complete sequence of Drosophila alpha-spectrin and show that it is similar to vertebrate nonerythroid spectrins. As in vertebrates, the alpha subunit consists of two large domains of repetitive sequence (segments 1-9 and 11-19) separated by a short nonrepetitive sequence (segment 10). The 106-residue repetitive segments are defined by a consensus sequence of 54 residues. Chicken alpha-spectrin (Wasenius, V.-M., M. Saraste, P. Salven, M. Eramaa, L. Holm, V.-P. Lehto. 1989. J. Cell Biol. 108:79-93) shares 50 of these consensus positions. Through comparison of spectrin and alpha-act

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Ryland, Elizabeth G., Yanhua Tang, Celia D. Christie, and Margaret E. Feeney. "Sequence Evolution of HIV-1 following Mother-to-Child Transmission." Journal of Virology 84, no. 23 (2010): 12437–44. http://dx.doi.org/10.1128/jvi.01617-10.

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ABSTRACT The genetic heterogeneity of HIV-1 poses a major obstacle to vaccine development. Although most horizontally acquired HIV-1 infections are initiated by a single homogeneous virus, marked genetic diversification and evolution occur following transmission. The relative contribution of the antiviral immune response to intrahost viral evolution remains controversial, in part because the sequence of the transmitted virus and the array of T-cell epitopes targeted by both donor and recipient are seldom known. We directly compared predominant viral sequences derived from 52 mother-child trans

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Jalbert, Louise, Elliot Rosen, Ann Lissens, Peter Carmeliet, Désiré Collen, and Francis Castellino. "Nucleotide Structure and Characterization of the Murine Gene Encoding Anticoagulant Protein C." Thrombosis and Haemostasis 79, no. 02 (1998): 310–16. http://dx.doi.org/10.1055/s-0037-1615006.

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SummaryThe 15,160 bp murine gene encoding anticoagulation protein C (PC) was cloned and sequenced, including 414 bp upstream of exon 1 and 80 bp downstream of the translation stop codon. Nine exons and eight introns were identified. The first exon was untranslated and contained the major transcriptional start site, the surrounding nucleotide sequence of which matched reasonably well with the consensus eukaryotic Cap element sequence. The translational initiator methio-nine residue was located in exon 2. The other introns were positioned as splices between the major domain units of the protein.

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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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Choi, Woo Suk, and Miguel Garcia-Diaz. "A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)." Nucleic Acids Research 50, no. 1 (2021): 322–32. http://dx.doi.org/10.1093/nar/gkab1230.

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Abstract Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are est

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