Index of /downloads/pfilt

 Name                    Last modified      Size  Description
 Parent Directory                             -   
 README                  31-Oct-2010 14:55  1.1K  
 pfilt.c                 01-Jul-2007 13:23  8.0K  
 test.fasta              01-Mar-2006 17:41  919   

This is the pfilt program, as described in the article:
Jones, D.T. & Swindells, M.B. (2002) Getting the most from PSI-BLAST. TIBS. 27: 161-164.

The pfilt program is designed to mask out (i.e. replace amino acid characters
with Xs) regions of low complexity, coiled-coil regions and regions with
extremely biased amino acid compositions. For compositional biased regions,
only the overrepresented amino acids are masked.

The program can be compiled as follows:

cc -O pfilt.c -lm -o pfilt

Usage: pfilt [-t] [-c] [-b] [-x] fasta-file

-t : turn off transmembrane masking
-c : turn off coiled-coil masking
-b : turn ON compositional masking
-x : turn off low-complexity masking
-f : exclude sequences with "fragment" in the description line

Note that the default is NOT to mask regions with biased composition!

The fasta-file can contain one or more sequences in standard FASTA format.


Change History
==============

1.0 : First release
1.1 : Added flag to turn off low-complexity filtering & changed defaults
1.2 : Minor bug fix
1.3 : Allow option to remove sequences described as being a "fragment"
1.4 : Increased buffer size and now checks for buffer overflows