Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.
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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
- To use use GeneSeqer_-5.0, import your data in ___ fasta format.
- Resources:http://replacewww.with.URL.for.tool.documentation.from.the.tool.source.orgplantgdb.org/tutorial/geneseqer.php
Test Data
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Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from Use testtrans.fa and genome.fa from the directory above as test input.
Parameters Used in in App
When the the app is 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.Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
- Default parameters only, no further configuration needed.
OR
- Use these parameters within the DE app interface:
- parameter name - value/setting
- parameter name - value/setting
Output File(s)
Expect a text a file named after the input files GeneSeqer_Out as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.
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Tool Source for App
- http://replacewww.with.URL.for.tool.orgplantgdb.org/cgi-bin/GeneSeqer/index.cgi