2012-01-10 Pan-genomes analysis is a hot topic in comparative genomics for bacterial genomes as it gives insights into species evolution, pathogenic mechanism, and epidemic diseases prevention. The new standalone program pan-genomes analysis pipeline (PGAP) has been developed by a research team led by Prof. YU Jun and Prof. XIAO Jingfa in Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS). PGAP integrates five analysis modules, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis, species evolution analysis and function enrichment analysis of gene clusters. As a result, it becomes more complete in genome research compared to other pan-genome analysis tools like Panseq or PGAT. It is developed with Perl script on the Linux Platform and its performance has been evaluated on 11 Streptococcus pyogenes strains. The time cost of running all tasks showed that it is effective and almost every section can be run on personal computer. “One of our major goals is to provide full automation of pan-genomes analysis workflow.” ZHAO Yongbing, a Ph.D. Candidate student said, ”Though it is not the first case to perform pan-genomes analysis in bioinformatics program, PGAP is a revolution of pipeline in genome analysis. It can perform five analytic functions with only one command, which will save users more time and energy.” The PGAP package is freely available from http://gpap.sf.net. This research was published online in Bioinformatics on Nov 29, 2011. PGAP: Pan-Genomes Analysis Pipeline. (Image by ZHAO Yongbing) Contact: Prof. YU Jun Email: junyu@big.ac.cn Prof. XIAO Jingfa Email: xiaojingfa@big.ac.cn 
