A Brief Review of Software Tools for Pangenomics

作     者：Jingfa Xiao Zhewen Zhang Jiayan Wu Jun Yu 

作者机构：CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2015年第13卷第1期

页      面：73-76页

核心收录：

学科分类：0710[理学-生物学] 0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 1001[医学-基础医学(可授医学、理学学位)] 07[理学] 08[工学] 0714[理学-统计学（可授理学、经济学学位）] 0703[理学-化学] 0701[理学-数学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：supported by the National High-tech R&D Program (863 Program Grant No. 2012AA020409) from theMinistry of Science and Technology of China the Key Program of the Chinese Academy of Sciences (Grant No. KSZD-EW-TZ-009-02) the National Natural Science Foundation of China (Grant Nos. 31471248 and 31271386) 

主　　题：Pangenomics Pangenome Comparative analysis Genomic dynamics Core genes 

摘      要：Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.