PMID:9813115
| Citation |
Robison, K, McGuire, AM and Church, GM (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284:241-54 |
|---|---|
| Abstract |
A major mode of gene regulation occurs via the binding of specific proteins to specific DNA sequences. The availability of complete bacterial genome sequences offers an unprecedented opportunity to describe networks of such interactions by correlating existing experimental data with computational predictions. Of the 240 candidate Escherichia coli DNA-binding proteins, about 55 have DNA-binding sites identified by DNA footprinting. We used these sites to construct recognition matrices, which we used to search for additional binding sites in the E. coli genomic sequence. Many of these matrices show a strong preference for non-coding DNA. Discrepancies are identified between matrices derived from natural sites and those derived from SELEX (Systematic Evolution of Ligands by Exponential enrichment) experiments. We have constructed a database of these proteins and binding sites, called DPInteract (available at http://arep.med.harvard.edu/dpinteract). |
| Links |
PubMed Online version:10.1006/jmbi.1998.2160 |
| Keywords |
Bacterial Proteins/metabolism; Binding Sites; Computational Biology/methods; DNA Footprinting; DNA, Bacterial/metabolism; DNA-Binding Proteins/metabolism; Databases, Factual; Escherichia coli/genetics; Genome, Bacterial; Molecular Sequence Data; Pattern Recognition, Automated; Protein Binding; Software |
| edit table |
Significance
You can help EcoliWiki by summarizing why this paper is useful
Useful Materials and Methods
You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.
Annotations
<annotationlinks/>
EcoliWiki Links
AlignACE
Category:Bioinformatics_Tools
Category:Databases
Category:DNA-binding_site_Databases
Category:E._coli_Databases
References
See Help:References for how to manage references in EcoliWiki.
