Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae
| Autor: | Rhonda Harrison, Charles DeLisi |
|---|---|
| Rok vydání: | 2002 |
| Předmět: |
Statistics and Probability
Quality Control Saccharomyces cerevisiae Proteins Saccharomyces cerevisiae Amino Acid Motifs Molecular Sequence Data Information Storage and Retrieval Computational biology Biochemistry Sensitivity and Specificity Fungal Proteins Open Reading Frames Intergenic region Sequence Analysis Protein Gene Expression Regulation Fungal Consensus Sequence Databases Genetic Binding site Databases Protein Molecular Biology Genetics Internet Binding Sites biology Base Sequence Quality assessment Reproducibility of Results biology.organism_classification Computer Science Applications DNA binding site DNA-Binding Proteins Computational Mathematics Computational Theory and Mathematics Database Management Systems Motif (music) Genome Fungal Sequence motif Sequence Alignment Protein Binding Transcription Factors |
| Zdroj: | Bioinformatics (Oxford, England). 18(10) |
| ISSN: | 1367-4803 |
| Popis: | Motivation: We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given factor. These sequences are multiply and locally aligned to give an anchor motif from which further characterization can take place. Results: We present bases for and assumptions about the variability within these motifs which give rise to potentially more accurate motifs, capture complex binding sites built upon the basis motif, and eliminate the constraints of the currently employed promoter searching protocols. We also present a measure of motif quality based on the occurrence of the putative motifs in regions observed to contain the binding sites. The assumptions, motif generation, quality assessment and comparison allow the user as much control as their a priori knowledge allows. Availability: IGRDB and the datasets mentioned herein are available at http://chipdb.wi.mit.edu/ Contact: rhonda@bu.edu * To whom correspondence should be addressed. |
| Databáze: | OpenAIRE |
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