PROKARYOTE GENE PREDICTION

PROKARYOTE GENE PREDICTION (PGP) is a bioinformatics pipeline for bacterial genome annotation.

PGP uses Prodigal for the ab initio gene prediction and automatically corrects starting codons with a strategy based on GenePrimp. PGP aligns gene products to bacterial proteins by BLAST, analyses the alignments, determines the need to shorten or elongate genes and introduces the required changes.

For each predicted gene, PGP identifies the function by searches in the Pfam, TIGRFAM, Hamap, PIRSF, PRINTS, SMART, SUPERFAMILY, ProSite and COG databases. The annotation results are organized into a gbk or gff file.

PROKARYOTE GENE PREDICTION can be applied to complete or draft genomes.