ArticleNucleic acids research1996
Searching databases of conserved sequence regions by aligning protein multiple-alignments.
Article in Nucleic acids research, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 98 papers.
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Who cites it
98 citing papers in PubMed.
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- Motifier: An IgOme Profiler Based on Peptide Motifs Using Machine Learning.Journal of molecular biology · 2021Article
- A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections.F1000Research · 2020Article
- A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package.Nucleic acids research · 2019Article
- TCR Fingerprinting and Off-Target Peptide Identification.Frontiers in immunology · 2019Article
- A systematic approach to RNA-associated motif discovery.BMC genomics · 2018Article
- Performance evaluation for MOTIFSIM.Biological procedures online · 2018Article
- Fast sequence analysis based on diamond sampling.PloS one · 2018Article
- Promoter shape varies across populations and affects promoter evolution and expression noise.Nature genetics · 2017Article
- Heterogeneity of transcription factor binding specificity models within and across cell lines.Genome research · 2016Article
- Comparative Protein Structure Modeling Using MODELLER.Current protocols in bioinformatics · 2016Article
- Article
- Analysis of Differentially Expressed Genes Associated With Alzheimer's Disease Based on Bioinformatics Methods.American journal of Alzheimer's disease and other dementias · 2015Article
- Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.Nucleic acids research · 2014Article
- MRFalign: protein homology detection through alignment of Markov random fields.PLoS computational biology · 2014Article
- Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier.Bioinformatics (Oxford, England) · 2013Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
1 author.
Funding
Abstract
A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions. Multiple alignments are treated as sequences of amino acid distributions and aligned by comparing pairs of such distributions. Four different comparison measures were tested and the Pearson correlation coefficient chosen. The method is sensitive, detecting weak sequence relationships between protein families. Relationships are detected beyond the range of conventional sequence database searches, illustrating the potential usefulness of the method. The previously undetected relation between flavoprotein subunits of two oxidoreductase families points to the potential active site in one of the families. The similarity between the bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA and Rad51 proteins likely to bind and unstack single-stranded DNA. Helix--turn--helix DNA binding domains from diverse proteins are readily detected and shown to be similar to each other. Glycosylasparaginase and gamma-glutamyltransferase enzymes are found to be similar in their proteolytic cleavage sites. The method has been fully implemented on the World Wide Web at URL: http://blocks.fhcrc.org/blocks-bin/LAMAvsearch.
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