msatcommander This open source application will help you locate microsatellite repeats, design locus-specific primers, and tag them
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search find locate find duplicates locate microsatellite nucleotide search

msatcommander Description

This open source application will help you locate microsatellite repeats, design locus-specific primers, and tag them msatcommander is a Python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatfinder will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).msatcommander will also tag and design primers using primer3 as its primer design engine. Here are some key features of "msatcommander": · searches for all mono-,di-,tri-,tetra-,penta-, and hexanucleotide repeats · repeats may be combined across user-specified distances (bp) · designs primers for located repeats · tags and tests primers with m13R, CAG, or custom tag. The 'best' primer is reported to the user · offers a convenient GUI for a majority of users · outputs results in csv format, for easy importation to spreadsheet software

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