PGAAS: a prokaryotic genome assembly assistant
system
Introduction:
In order to accelerate the finishing phase of
genome assembly, especially for the whole genome shotgun approach
of prokaryotic species, we have developed a software package
designated prokaryotic genome assembly assistant system (PGAAS).
The approach upon which PGAAS is based is to confirm the order
of contigs and fill gaps between contigs through peptide links
obtained by searching each contig end with BLASTX against protein
database.
We used the contig dataset of the cyanobacterium Synechococcus
sp. Strain PCC7002 (PCC7002), which was sequenced with six-fold
coverage and assembled using the Phrap package. The subject
database is the protein database of the cyanobacterium, Synechocystis
sp. Strain PCC6803 (PCC6803). We found more than 100 non-redundant
peptide segments which can link at least 2 contigs. We tested
one pair of linked contigs by sequencing and obtained satisfactory
result. PGAAS provides a graphic user interface to show the
bridge peptides and pier contigs. We integrated Primer3 into
our package to design PCR primers at the adjacent ends of the
pier contigs.
We tested PGAAS on a linux (Redhat 6.2) PC machine; it is developed
with free software (MySQL, PHP and Apache). The whole package
is distributed freely and can be downloaded as UNIX compress
file.
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