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Infernal Stage 4 (cmsearch)
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Searches a sequence database for RNAs homologous to a covariance model.
Quick Start
- To use Infernal Stage 4 (cmsearch), import a covariance model file in .cm format and a sequence file in FASTA format.
- Resources: http://infernal.janelia.org/
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> cmsearch.
Input File(s)
Use my.c.cm and tosearch.300Kb.db 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 text file with high-scoring alignments as output. For the test case, the output file you will find in the example_data directory is named highscoringhits.txt.