Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data
| Autor: | Michael J. Palumbo, Lee A. Newberg |
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| Rok vydání: | 2010 |
| Předmět: |
Transcription
Genetic Gene prediction 0206 medical engineering CAAT box 02 engineering and technology Computational biology Biology Conserved sequence User-Computer Interface 03 medical and health sciences Upstream activating sequence Genetics Promoter Regions Genetic Enhancer 030304 developmental biology Internet 0303 health sciences Binding Sites General transcription factor Sequence Analysis DNA Articles DNA binding site Gene Expression Regulation TRANSFAC Sequence Alignment Software 020602 bioinformatics Transcription Factors |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkq330 |
| Popis: | The transcription of a gene from its DNA template into an mRNA molecule is the first, and most heavily regulated, step in gene expression. Especially in bacteria, regulation is typically achieved via the binding of a transcription factor (protein) or small RNA molecule to the chromosomal region upstream of a regulated gene. The protein or RNA molecule recognizes a short, approximately conserved sequence within a gene's promoter region and, by binding to it, either enhances or represses expression of the nearby gene. Since the sought-for motif (pattern) is short and accommodating to variation, computational approaches that scan for binding sites have trouble distinguishing functional sites from look-alikes. Many computational approaches are unable to find the majority of experimentally verified binding sites without also finding many false positives. Phyloscan overcomes this difficulty by exploiting two key features of functional binding sites: (i) these sites are typically more conserved evolutionarily than are non-functional DNA sequences; and (ii) these sites often occur two or more times in the promoter region of a regulated gene. The website is free and open to all users, and there is no login requirement. Address: (http://bayesweb.wadsworth.org/phyloscan/). |
| Databáze: | OpenAIRE |
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