Bioinformatics and Biological Databases: 1) Sigma-54 Promoter Database – A Database of Sigma-54 Promoters Covering a Wide Range of Bacterial Genomes 2) ClusterMine360 – A Database of PKS/NRPS Biosynthesis

Abstract

The Sigma-54 Promoter Database contains computationally predicted sigma-54 promoters from over 60 prokaryotic species. Organisms from all major phyla were analysed and results were made available online at http://www.sigma54.ca. This database is particularly unique due to its inclusion of intragenic regions, grouping of data by COG and COG category, and the ability to summarize results either by phylum or database-wide. ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and nonribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has over 200 gene clusters from over 185 compound families. It also features a unique sequence repository containing over 10,000 PKS/NRPS domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. This database will be a useful resource for members of the PKS/NRPS research community enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information.