Prediction of bacterial promoters
Algorithm predicts potential transcription start positions of bacterial genes regulated by sigma70 promoters (major E.coli promoter class). Linear discriminant function (LDF) combines characteristics describing functional motifs and oligonucleotide composition of these sites. BProm has accuracy of E.coli promoter recognition about 80%. Its specificity is also about 80% when tested on sets containing promoter and non-promoter sequences in equal numbers. It is not advisable to run BProm on whole genomes. To increase specificity, run BProm on a region between two neighboring ORFs located on the same strand, or on a sequence upstream from an ORF, keeping in mind that most promoters are located within 150 bp region from protein coding sequence.