title: GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.
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.
authors: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan. d9662841@oz.nthu.edu.tw
authors: Chi-Ching
authors: CC
authors: Lee
authors: Yi-Ping Phoebe
authors: YP
authors: Chen
authors: Tzu-Jung
authors: TJ
authors: Yao
authors: Cheng-Yu
authors: CY
authors: Ma
authors: Wei-Cheng
authors: WC
authors: Lo
authors: Ping-Chiang
authors: PC
authors: Lyu
authors: Chuan Yi
authors: CY
authors: Tang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D004926:Escherichia coli / Q000235:genetics; D005827:Genetics, Microbial / Q000379:methods*; D016678:Genome; D016680:Genome, Bacterial; D044404:Genomic Islands; D058977:Molecular Sequence Annotation / Q000379:methods*; D019779:Salmonella enterica / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface