GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects |
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| Authors: | Chi-Ching Lee Yi-Ping Phoebe Chen Tzu-Jung Yao Cheng-Yu Ma Wei-Cheng Lo Ping-Chiang Lyu Chuan Yi Tang |
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| Affiliation: | 1. Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan;2. Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan;3. Department of Computer Science and Computer Engineering, La Trobe University, Melbourne, Australia;4. Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan;5. Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan;6. Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan;g Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan |
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| 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. |
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| Keywords: | GI, genomic island GI-POP, genomic island prediction by Genome Profile Scanning GI-GPS, genomic island genomic profile scanning HGT, horizontal gene transferring DNA, deoxyribonucleic acid %G + C, guanine and cytosine contents PCR, polymerase chain reaction tRNA, transfer RNA COG, clusters of Orthology Groups DIYA, do-it-yourself annotator CDS, coding sequences CDD, conserved domain databases SWS, sliding window scanning SVM, support vector machine MGE, mobile genetic elements CAI, codon adaption indices E. coli, Escherichia coli ROC, receiver-operating characteristic AUC, area under curve PE, probabilistic estimate S. enterica, Salmonella enterica NCBI, National Center of Biotechnology Information PHP, PHP: hypertext preprocessor RBF, radial basis function ACC, accuracy USD, unique signature-discovering PAI, pathogenicity island |
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