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Bioinformatics Advance Access originally published online on February 3, 2005
Bioinformatics 2005 21(9):2083-2084; doi:10.1093/bioinformatics/bti176
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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,*

1Bioscience Division, Los Alamos National Laboratory Los Alamos, NM 87545, USA
2Counterterrorism and Forensic Science Research Unit, FBI Academy Quantico, VA 22135, USA

*To whom correspondence should be addressed.

Summary: Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variations in 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 SNP 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 ongoing sequencing projects for SNP prediction. SNPsFinder will use genome sequence annotation if available and map the predicted SNP 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 SNP regions according to user's input parameters to facilitate experimental validation. The results from SNPsFinder analysis are accessible through the World Wide Web.

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

Contact: murray{at}lanl.gov

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


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