Comparative analysis of regulatory patterns in bacterial genomes

@article{citeulike:2535301, abstract = {Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult problem. There are no algorithms capable of making reliable predictions even for well-studied sites such as the CRP (cyclic AMP receptor protein) box. However, availability of complete bacterial genomes makes it possible to make reliable predictions with bad rules. This comparative approach is based on the assumption that sets of co-regulated genes are conserved in related bacteria. Thus true sites occur upstream of orthologous genes, whereas false candidates are scattered at random. This means not only that knowledge about regulation in well-studied genomes can be transferred to newly sequenced ones, but also that new members of regulons can be found. This paper reviews several recent studies. In particular, a detailed analysis of catabolite repression in gamma-purple bacteria is presented. 10.1093/bib/1.4.357}, author = {Gelfand, Mikhail S. and Novichkov, Pavel S. and Novichkov, Elena S. and Mironov, Andrey A. }, citeulike-article-id = {2535301}, doi = {http://dx.doi.org/10.1093/bib/1.4.357}, journal = {Brief Bioinform}, keywords = {survey}, month = {January}, number = {4}, pages = {357--371}, posted-at = {2008-03-15 02:29:19}, priority = {2}, title = {Comparative analysis of regulatory patterns in bacterial genomes}, url = {http://dx.doi.org/10.1093/bib/1.4.357}, volume = {1}, year = {2000} }

TY - JOUR ID - citeulike:2535301 L3 - citeulike-article-id:2535301 TI - Comparative analysis of regulatory patterns in bacterial genomes JF - Brief Bioinform VL - 1 IS - 4 SP - 357 EP - 371 N2 - Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult problem. There are no algorithms capable of making reliable predictions even for well-studied sites such as the CRP (cyclic AMP receptor protein) box. However, availability of complete bacterial genomes makes it possible to make reliable predictions with bad rules. This comparative approach is based on the assumption that sets of co-regulated genes are conserved in related bacteria. Thus true sites occur upstream of orthologous genes, whereas false candidates are scattered at random. This means not only that knowledge about regulation in well-studied genomes can be transferred to newly sequenced ones, but also that new members of regulons can be found. This paper reviews several recent studies. In particular, a detailed analysis of catabolite repression in gamma-purple bacteria is presented. 10.1093/bib/1.4.357 KW - survey AU - Gelfand, Mikhail AU - Novichkov, Pavel AU - Novichkov, Elena AU - Mironov, Andrey PY - 2000/01/01/ UR - http://dx.doi.org/10.1093/bib/1.4.357 ER -