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

Chi Ching Lee, Yi Ping Phoebe Chen, Tzu Jung Yao, Cheng Yu Ma, Wei Cheng Lo, Ping Chiang Lyu*, Chuan Yi Tang

*此作品的通信作者

研究成果: 期刊稿件文章同行評審

15 引文 斯高帕斯(Scopus)

摘要

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.

原文英語
頁(從 - 到)114-123
頁數10
期刊Gene
518
發行號1
DOIs
出版狀態已出版 - 10 04 2013
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