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Bioinformatics Advance Access published online on February 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti176
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received October 5, 2004
Accepted November 22, 2004

Applications note

SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes

Jian Song 1*, Yan Xu 1, Scott White 1, Kevin W. P. Miller 2, and Murray Wolinsky 1

1 Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
2 Counterterrorism and Forensic Science Research Unit, FBI Academy, Quantico, Virginia 22135

* To whom correspondence should be addressed.
Jian Song, E-mail: jian{at}lanl.gov


  Abstract

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variations among closely related microbial species, strains or isolates. Some SNPs confer selective advantages for microbial pathogens during infection and many others are powerful genetic markers for distinguishing closely related strains or isolates that could not be distinguished otherwise. To facilitate SNPs discovery in microbial genomes, we have developed a web-based application, SNPsFinder, for genome-wide identification of SNPs. SNPsFinder takes multiple genome sequences as input to identify SNPs within homologous regions. It can also take contig sequences and sequence quality scores from on-going sequencing projects for SNPs prediction. SNPsFinder will use genome sequence annotation if available and map the predicted SNPs regions to known genes or regions to assist further evaluation of the predicted SNPs for their functional significance. SNPsFinder can generate PCR primers for all predicted SNPs regions according to user's input parameters to facilitate experimental validation. The results from SNPsFinder analysis will be accessible through the World Wide Web.

Availability: The SNPsFinder program is available at http://snpsfinder.lanl.gov/.

Supplementary Information: The user's manual is available at http://snpsfinder.lanl.gov/UsersManual/.


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