文章基本信息

标题：SNIT: SNP identification for strain typing
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作者：Ravi Vijaya Satya ; Nela Zavaljevski ; Jaques Reifman 等
期刊名称：Source Code for Biology and Medicine
印刷版ISSN：1751-0473
电子版ISSN：1751-0473
出版年度：2011
卷号：6
期号：1
页码：14
DOI：10.1186/1751-0473-6-14
语种：English
出版社：BioMed Central
摘要：With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html
关键词：Close Neighbor ; Pairwise Alignment ; Bacillus Anthracis ; Yersinia Pestis ; Francisella Tularensis