Narrow PSSMs

# Blocks WWW Server

A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA.

This page will convert a narrow block , frequency or weight PSSM to BLIMPS and MAST format and then search it vs Swiss-Prot using BLIMPS.
The conversion is done as follows:

- If a block is input, equal sequence weights are used.
- If a block is input, amino acid frequencies are computed for each position.
- If a block or frequency PSSM is input, minimal pseudo counts are added to the actual counts; just enough to allow log-odds to be computed. For a block, 1 pseudo-count per 10,000 real counts is computed using a substitution matrix. For a frequency PSSM, 10,000 real counts and 1 pseudo-count are assumed and the pseudo-count is computed using background frequencies.
- If a block or frequency PSSM is input, the expected values for the odds ratios are taken from Swiss-Prot and the log base e (scale in nats) of the odds ratios is computed.
- This PSSM is output in MAST format.
- This PSSM is converted to a positive matrix and output in BLIMPS format.

  If you have a multiple alignment, you can reformat it as a BLOCK.

  Select a query type:

  Enter the name of a file containing your query:
  -or-
  Enter your query:

  Contact us

  Page last modified on Mar 2003