Zhou Yu1, Tao Li, Jindong Zhao, Jingchu Luo. 1. College of Life Sciences, The National Key Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China.
Abstract
MOTIVATION: 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 databases. RESULTS: 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. AVAILABILITY: 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: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.
MOTIVATION: 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 databases. RESULTS: 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. AVAILABILITY: 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: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.
Authors: Sander A Peters; Jan C van Haarst; Taco P Jesse; Dennis Woltinge; Kim Jansen; Thamara Hesselink; Marjo J van Staveren; Marleen H C Abma-Henkens; René M Klein-Lankhorst Journal: Plant Physiol Date: 2006-03 Impact factor: 8.340