Phage_Finder-
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Phage_Finder was developed at The
Institute for Genomic Research (TIGR)
by Dr. Derrick E. Fouts as a heuristic computer program
written in PERL
to identify prophage
regions within bacterial genomes (In press Nucleic Acids
Research, 2006).
It uses tab-delimited results from NCBI
BLASTALL or WU
BLASTP 2.0 searches against a
collection of bacteriophage protein sequences and results
from HMMSEARCH
analysis of 441 phage-specific HMMs to locate prophage
regions. By using FASTA33,
MUMMER
or BLASTN,
it can find potential attachment (att) sites of the phage
region(s). Data from tRNAscan-SE
and Aragorn
are used to determine whether a tRNA
or tmRNA
served as the putative target for integration. Additionally,
by looking for the presence or absence of specific proteins
using specific HMM models, Phage_Finder can predict whether
the region is most likely prophage and which type
(Mu,
P2, or retron R73),
an integrated element, a plasmid,
or a degenerate phage region.
The goal of this project is to provide an open-sourced,
standardized and automated system to identify and classify
prophages within prokaryotic
genomes. It is hoped that this package will facilitate
future studies on the biology and evolution of these
prophages by providing a level of microbial genome
annotation that was previously void.
See results
from searching 302
bacterial genomes.
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