PGAAS: a prokaryotic genome assembly assistant system

doi:10.1093/bioinformatics/18.5.661

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	PGAAS: a prokaryotic genome assembly assistant system
	Yu, Z ; Li, T ; Zhao, JD ; Luo, JC
刊名	bioinformatics
	2002
关键词	TOOL
DOI	10.1093/bioinformatics/18.5.661
英文摘要	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.; Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability; SCI(E); 6; 5; 661-665; 18
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/388284]
专题	生命科学学院
推荐引用方式 GB/T 7714	Yu, Z,Li, T,Zhao, JD,et al. PGAAS: a prokaryotic genome assembly assistant system[J]. bioinformatics,2002.
APA	Yu, Z,Li, T,Zhao, JD,&Luo, JC.(2002).PGAAS: a prokaryotic genome assembly assistant system.bioinformatics.
MLA	Yu, Z,et al."PGAAS: a prokaryotic genome assembly assistant system".bioinformatics (2002).