ssrFinder.pl is used to develop Simple Sequence Repeat (SSR) markers from a list of query DNA sequences provided in FASTA format.

It uses a regular expression to identify all SSR motifs along the input sequences.

Any tract of repetitive DNA in which a k-mer of length k repeated at least n times will be labeled as a potential SSR marker:
k=1, n>=12 ex: AAAAAAAAAAAA
k=2, n>=6 ex: ATATATATATAT
k=3, n>=4 ex: ATCATCATCATC
k=4, n>=3 ex: ATCGATCGATCG

For each SSR identified in the list of query sequences, the script is able to design a pair of primers located on each side of the repeated motif.

These primer sequences can then be used for DNA amplification by Polymerase Chain Reaction (PCR).

Etablishment : I.N.R.A.

Tags: Primer, SSR, Perl

This project has not yet categorized itself in the Trove Software Map Registered: 2015-06-03 15:50
Activity Ranking: 127
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