isbpFinder is a Perl script dedicated to design ISBP (Insertion Site Based Polymorphism) markers.

It allows the creation of features representing primers/amplicons covering the junction between 2 transposable elements (TEs) in order to obtain a graphical view of the different markers designed by viewing the feartures through a sequence annotation software such as "Artemis".

isbpFinder can generate output files in CSV, EMBL and GFF format containing TEs and amplicons/primers.

IsbpFinder is based on the following programs:
- "RepeatMasker" for TE detection
- "Primer3" for primer design for TE junction amplification.

For more details about ISBP markers, please read "Paux et al., Plant Biotechnology Journal 2010(8):196-210" ( [url=http://www.ncbi.nlm.nih.gov/pubmed/20078842]test[/url] )

Etablishment : I.N.R.A.

Tags: ISBP, Primer, TE, Perl

This project has not yet categorized itself in the Trove Software Map Registered: 2015-06-03 16:00
Activity Ranking: 241
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