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[ Source: glam2  ]

Package: glam2 (1058-1)

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 — for discovering motifs shared by a set of sequences; glam2scan — for finding matches, in a sequence database, to a motif discovered by glam2; glam2format — for converting glam2 motifs to standard alignment formats; glam2mask — for masking glam2 motifs out of sequences, so that weaker motifs can be found; glam2-purge — for 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

  • depends
  • recommends
  • suggests
  • dep: libc0.1 (>= 2.7-1) [kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.7-1) [hurd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.7-1) [not alpha, hurd-i386, ia64, kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libc6.1 (>= 2.7-1) [alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
  • dep: libfftw3-3
    library for computing Fast Fourier Transforms

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Architecture Package Size Installed Size Files
alpha 267.0 kB616 kB [list of files]
amd64 251.3 kB548 kB [list of files]
arm 235.8 kB512 kB [list of files]
armel 249.1 kB536 kB [list of files]
hppa 256.2 kB556 kB [list of files]
hurd-i386 234.4 kB508 kB [list of files]
i386 237.3 kB508 kB [list of files]
ia64 307.2 kB748 kB [list of files]
kfreebsd-amd64 (unofficial port) 248.0 kB462 kB [list of files]
kfreebsd-i386 (unofficial port) 234.3 kB424 kB [list of files]
mips 258.3 kB608 kB [list of files]
mipsel 254.2 kB608 kB [list of files]
powerpc 249.7 kB568 kB [list of files]
s390 248.0 kB548 kB [list of files]
sparc 234.6 kB520 kB [list of files]