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Accession Number ADA571154
Title SNIT: SNP Identification for Strain Typing.
Publication Date 2011
Media Count 6p
Personal Author J. Reifman N. Zavaljevski R. V. Satya
Abstract 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.
Keywords Bacteria
Computer programs
Genome
Identification
Nucleotides
Pipelines
Polymorphism
Snit(Snp identification for strain typing)
Snp(Single nucleotide polymorphisms)
Strains(Biology)


 
Source Agency Non Paid ADAS
NTIS Subject Category 57B - Biochemistry
57E - Clinical Medicine
Corporate Author Army Medical Research and Materiel Command (Provisional), Fort Detrick, MD. Telemedicine and Advanced Tech Research Center.
Document Type Journal article
Title Note Journal article.
NTIS Issue Number 1315
Contract Number N/A

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