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BLASTX (HPC)
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Community rating: ?????
BLASTX contig assemblies or metagenome samples against an iPlant-maintained NCBI database mirror using TACC Ranger. Designed for query files of up to 500k sequences with estimated turnaround time of 24h.
Quick Start
- To use BLASTX (HPC), import your data in ___ format.
- Resources: http://replace.with.URL.for.tool.documentation.from.the.tool.source.org
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 -> directory. |
Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt 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.
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 file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.
Tool Source for App
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The BLASTX apps have been removed from the Discovery Environment, because they were used much too heavily, thus causing a strain on our infrastructure. BLASTX is not the preferred method for annotating transcript assemblies, even though it is still commonly used for this purpose. We recommend using Transcript decoder to create 1 good translation of your nucleotide contigs and then use that translation to Blastp against an appropriately select database. Using this approach gives the user better, more appropriate results, and saves the drain of our computation time. A good tool for performing the Blastp step is the app Blastp a subset of Uniprot, which was created specifically for annotation.
If the user prefers still to use Blastx, we recommend using a desktop or laptop computer with Blastx installed. Installation and running of Blast applications is not that difficult for those new to bioinformatics.