Overview

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).

Reference

Yoji NAKAMURA, Yuya SHIGENOBU, Takuma SUGAYA, Tadahide KUROKAWA, Kenji SAITOH (2012) Automated screening and primer design of fish microsatellite DNA loci on pyrosequencing data, Ichthyological Research (2012), DOI: 10.1007/s10228-012-0317-8.

Contact Email

FRA-bioinfo@ml.affrc.go.jp