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  • SNPT - Single Nucleotide Polymorphism Typing data analysis tool

    Sample Input | Download (1.2 MB Zip File) | Publication
    Instructions

    SNPT (Single Nucleotide Polymorphism Typing) is a Perl application developed by Weihong Qi at Dr. Tom Whittam's Microbial Evolution Laboratory at Michigan State University.

    The script reads in a text file containing multilocus SNPs data. Types of data analysis includes:

  • Indentify unique SNPs profiles and assign sequence types(MST);
  • Calculate allele frequencies;
  • Find informative SNPs;
  • Calculate D (Index of the Discrininatory Ability);
  • Find the set(s) of minimum SNPs;
  • Output MST data file in mega and interleaved mega format.
  • Input data should be in tab-delimited flat text format. The first line is the genomic location of each snp. The second line is indexed by the strain name, followed by each SNP.
    Example of input data:
    Strain 325 968 2351 4768 4980 6971 9323 1319
    ARK0000038 G C C G G A G T
    ARK0000056 G C C G G A G T
    ARK0000062 G C C G G A G T
    ARK0000066 G C C G G A G T
    ARK0000069 G C T G G A G T
    ...

    Contact stec@cvm.msu.edu
    Operated by Shannon D. Manning at Michigan State University