Intron Marker Pipeline Design of intron flanking primers using ESTs as a template in species with limited to no genomic sequence
Download

Intron Marker Pipeline Ranking & Summary

Intron Marker Pipeline Tags

sequence Intron Marker Pipeline Expressed Sequence Tags EST sequence EST Intron

Intron Marker Pipeline Description

Design of intron flanking primers using ESTs as a template in species with limited to no genomic sequence The Intron Marker Pipeline (IMP) pipeline has been developed as an automated tool for design of primers which flank predicted intron location in Expressed Sequence Tags (ESTs). The Intron Marker Pipeline (IMP) aims to describe the species with limited to no genomic sequence data available. All that is required for input is a FASTA file containing the EST sequence and another FASTA file containing any genomic sequence to be used for intron prediction. This allows optimal flexibility for users, allowing them to control the exact sequences used. Installation Instructions: · Download the current distribution · Unpack (will create it’s own containing folder) using tar –zxvf filename in the terminal · Install ReapeatMasker, BLAT, GeneSeqer and Primer3 command line utilities and note down the path to and including the executable for each one (ex:/usr/local/share/applications/Primer3/src/primers_core) · Run perl install.pl in the base directory of IMP · Enter the paths already noted down when prompted Requirements: · RepeatMasker · BLAT · GeneSeqer · Primer3 command-line utility

Intron Marker Pipeline Related Software