| glam2 | gapped protein motifs from unaligned sequences | Mehr ... |
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.
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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.
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In this package, the fast Fourier algorithm (FFT) was enabled for glam2.
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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). |
