Purge removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618--1632, 1995.
Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.
purge examples/lipocalin.s 150
purge examples/crp0.s 175
usage: purge file score
options: [-n] - sequences are DNA (default: protein) [-b] - use blast heuristic method (default for protein) [-e] - use an exhaustive method (default for DNA) [-q] - keep first sequence in the set [-x] - use xnu to mask protein tandem repeats Purge creates an output file from the input file such that no two sequences have local alignment score greater than . The output file is named . . Substitution matrices: BLOSUM62 (protein), +5/-1 (DNA).