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Gene. 2013 Apr 10;518(1):114-23. doi: 10.1016/j.gene.2012.11.063. Epub 2013 Jan 12.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

Author information

1
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan. d9662841@oz.nthu.edu.tw

Abstract

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project.

PMID:
23318308
DOI:
10.1016/j.gene.2012.11.063
[Indexed for MEDLINE]
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