Package: glam2 (1064-1)
Links for glam2
Download Source Package glam2:
- Debian-Med Packaging Team (QA Page, Mail Archive)
- Steffen Moeller (QA Page)
- Charles Plessy (QA Page)
- Homepage [bioinformatics.org.au]
gapped protein motifs from unaligned sequences
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.
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 package, the fast Fourier algorithm (FFT) was enabled for glam2.
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).
Other Packages Related to glam2