glam2-purge1

Usage

Overview

glam2-purge is a modified version of Andrew Neuwald´s purge program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. 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 output file is named <file>.<score>. 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.

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.

References

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. Please cite it if you use Purge.

If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).