Intron Marker PipelineDesign of intron flanking primers using ESTs as a template in species with limited to no genomic sequence | |
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Intron Marker Pipeline Ranking & Summary
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- License:
- GPL
- Price:
- FREE
- Publisher Name:
- Intron Marker Pipeline Team
- Publisher web site:
- http://code.google.com/p/intron-marker-pipeline/people/list
- Operating Systems:
- Mac OS X
- File Size:
- 197 KB
Intron Marker Pipeline Tags
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
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