Auto-Primer
©
Yoji Nakamura
December 6, 2012
Version 1.0
Auto-primer is a pipeline that predicts microsatellite repeats in nucleotide sequences and design the detection primers. It automatically runs two programs,
Tandem repeats finder (Benson, 1999) and
Primer3 (Rozen & Skaletsky, 2000)
(these are not bundled in Auto-primer), parses the outputs,and finally generates a primer list. In particular, this pipeline is a powerful tool for handling high-throughput genomic sequences produced by next-generation sequencing platforms. Auto-primer is written in Perl and available at a web page. Auto-primer originally runs on a Linux computer (e.g.
CentOS). It needs two programs installed (Tandem repeats finder and Primer3). It is portable to Windows PC (MS-DOS), if it has a Perl environment installed (e.g.
ActivePerl).
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