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NCBI BLAST+ makeprofiledb (version 2.14.1+galaxy2)

Input PSSM files(s):

One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)

Title for the profile database:

This is the database name shown in BLAST search output

Minimum word score to add a word to the lookup table:

Does your input file contain PSSM scores?:

Exclude invalid domains?:

Exclude domains that do not pass validation test

Observation threshold:

Exclude domains with with maximum number of independent observations below this threshold

What it does

Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN) from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI "scoremat" ASN.1 format (usually named *.smp).

This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'.

More information about makeprofiledb can be found in the BLAST Command Line Applications User Manual.

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). NCBI BLAST+ integrated into Galaxy. GigaScience 4:39 https://doi.org/10.1186/s13742-015-0080-7

Christiam Camacho et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 15;10:421. https://doi.org/10.1186/1471-2105-10-421

This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus