VIGOR extended to annotate genomes for additional 12 different viruses.
VIGOR extended to annotate genomes for additional 12 different viruses.
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DOI：
10.1093/nar/gks528
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Stockwell TB
中科院分区：
文献类型：
--
作者：
Wang S;Sundaram JP;Stockwell TB
基因预测程序VIGOR（病毒基因组ORF阅读器）于2010年在J.克雷格文特尔研究所开发，并已成功地为传染病基因组测序中心的项目在冠状病毒、流感、鼻病毒和轮状病毒中进行基因调用。VIGOR使用针对定制蛋白质数据库的序列相似性搜索来识别蛋白质编码区、起始密码子和终止密码子以及其他基因特征。基于序列相似性和特征残基准确鉴定核糖核酸编辑和其他特征。VIGOR生成四个输出文件：基因预测文件、互补DNA文件、比对文件和基因特征表文件。基因特征表可用于创建GenBank提交。VIGOR采用单一输入：FASTA格式的病毒基因组序列。VIGOR已扩展到预测12种病毒的基因：麻疹病毒、腮腺炎病毒、风疹病毒、呼吸道合胞病毒、甲病毒和委内瑞拉马脑炎病毒、诺如病毒、偏肺病毒、黄热病病毒、日本脑炎病毒、副流感病毒和仙台病毒。VIGOR可以准确地检测复杂的基因特征，如核糖核酸编辑、终止密码子泄漏和核糖体分流。精确识别某些病毒的mat_peptide切割是VIGOR的内置功能。这些病毒的基因预测已经通过测试来自GenBank的27至240个基因组进行了评估。
A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately identified based on sequence similarity and signature residues. VIGOR produces four output files: a gene prediction file, a complementary DNA file, an alignment file, and a gene feature table file. The gene feature table can be used to create GenBank submission. VIGOR takes a single input: viral genomic sequences in FASTA format. VIGOR has been extended to predict genes for 12 viruses: measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus and Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus and Sendai virus. VIGOR accurately detects the complex gene features like ribonucleicacid editing, stop codon leakage and ribosomal shunting. Precisely identifying the mat_peptide cleavage for some viruses is a built-in feature of VIGOR. The gene predictions for these viruses have been evaluated by testing from 27 to 240 genomes from GenBank.
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