PGAAS: a prokaryotic genome assembly assistant system.

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Genome assembly, particularly for prokaryotic species using the whole genome shotgun approach, requires efficient finishing methods.
• Current methods can be time-consuming, necessitating the development of specialized software to accelerate this critical phase.

Purpose of the Study:

• To develop a software package, the Prokaryotic Genome Assembly Assistant System (PGAAS), to expedite the genome assembly finishing process.
• To utilize peptide links derived from protein database searches to confirm contig order and bridge gaps in genome sequences.

Main Methods:

• PGAAS employs BLASTX searches of contig ends against protein databases to identify peptide links.
• The software analyzes these peptide links to establish contig order and identify gaps.
• A graphical user interface visualizes linking peptides and contigs, with integrated Primer3 for PCR primer design.

Main Results:

• Applied to Synechococcus sp. strain PCC7002 genome data, PGAAS identified over 100 non-redundant peptide segments linking contigs.
• Experimental validation of a linked contig pair yielded satisfactory sequencing results.
• The system successfully designed PCR primers for adjacent contig ends.

Conclusions:

• PGAAS effectively uses peptide links to order contigs and fill gaps in prokaryotic genome assembly.
• The software provides a user-friendly interface and integrates primer design tools, enhancing the genome finishing pipeline.
• PGAAS is freely available, developed using open-source software, and continually updated.