PGA4genomics for comparative genome assembly based on genetic algorithm optimization.
New sequencing technologies greatly facilitate the large-scale bacterial genome sequencing by reducing cost. However, a considerable bottleneck is in the finishing phase, where dozens to hundreds of gaps need to be closed. In this study, we constructed a web server (PGA4genomics) to help users automate gap closing based on comparative genomic syntenies. Extensive evaluations showed that it significantly outperforms previous methods and can produce highly accurate layout result, especially when assembling genomes that are only moderately related. The availability of such a platform would greatly benefit the research community working on bacterial genomics. PGA4genomics can be accessed at two mirror sites http://centre.bioinformatics.zj.cn:8080/pga or http://59.79.168.90:8080/pga.
Zhao
Fangqing
F
Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325035, China. fuz3@psu.edu
Hou
Huabin
H
Bao
Qiyu
Q
Wu
Jinyu
J
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D020451:Contig Mapping; D017931:DNA Primers; D004269:DNA, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D017422:Sequence Analysis, DNA; D026801:Synteny; D014584:User-Computer Interface
D017931:DNA Primers; D004269:DNA, Bacterial