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


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


BACKGROUND
The user's manual is available at http://snpsfinder.lanl.gov/UsersManual/
Song
Jian
J
Bioscience Division, Los Alamos National Laboratory, NM 87545, USA.
Xu
Yan
Y
White
Scott
S
Miller
Kevin W P
KW
Wolinsky
Murray
M
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D016680:Genome, Bacterial; D016681:Genome, Fungal; D020407:Internet; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface