glam2

GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. This package includes programs for discovering motifs shared by a set of sequences and finding matches to these motifs in a sequence database, as well as utilities for converting glam2 motifs to standard alignment formats, masking glam2 motifs out of sequences so that weaker motifs can be found, and removing highly similar members of a set of sequences. The package includes these programs: glam2: discovering motifs shared by a set of sequences; glam2scan: finding matches, in a sequence database, to a motif discovered by glam2; glam2format: converting glam2 motifs to standard alignment formats; glam2mask: masking glam2 motifs out of sequences, so that weaker motifs can be found; glam2-purge: removing highly similar members of a set of sequences. In this binary package, the fast Fourier algorithm (FFT) was enabled for the glam2 program.