The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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GeneSeqer-5.0

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GeneSeqer maps ESTs and contigs against a genome sequence, producing gapped alignments and proposed exon structures for the genes that are covered.

There are 3 versions of this app --  tiny, medium, and large. These run on 16, 64, and 128 cores on the Stampede server at TACC. Take a guess and match your transcript file and genome size to number of cores.

Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> geneseqer

Input File(s)

Use testtrans.fa and genome.fa from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a file named GeneSeqer_Out as output. 

Tool Source for App

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