MakePSSM

MakePSSM is a PSC developed program that allows users to easily create Position Specific Scoring Matrix (PSSMs, profiles) from a Multiple Sequence File (MSF). Currently there are three algorithms available to create the PSSM:

  • straight log-odds computation (appropriate when a user has over 300 sequences aligned)
  • and two methods for situations where there is insufficient data to compute the log-odds table:
    • implicit pseudo-counts as developed by Gribskov and Eisenberg, and
    • an explicit pseudo-count method developed by Henikoff and Henikoff.

For both methods, there are a number of matrices and underlying mutational frequencies available for the computation of the PSSM.

Installed on the Opteron cluster.

Opteron usage

It is convenient to use /biomed/lib/examples/.login.fixed for this and other sequence analysis packages.

/biomed/bin/MakePSSM

gives an extensive introduction and help. Typical usage would be:

/biomed/bin/MakePSSM -i infile -a approach -m matrix  \
  -g gap-model  -r start  end -o outfile

For a description of the options, see the MakePSSM Userguide.

See also: