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Package: glam2 (1064-1)

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:       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

  • 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 (>= 2.5-5) [m68k]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.7-1) [not alpha, hurd-i386, ia64, kfreebsd-amd64, kfreebsd-i386, m68k]
  • 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

Download glam2

Download for all available architectures
Architecture Package Size Installed Size Files
alpha 264.5 kB616 kB [list of files]
amd64 251.9 kB548 kB [list of files]
arm 241.5 kB512 kB [list of files]
armel 246.5 kB536 kB [list of files]
hppa 255.7 kB556 kB [list of files]
hurd-i386 235.0 kB508 kB [list of files]
i386 234.8 kB460 kB [list of files]
ia64 307.0 kB756 kB [list of files]
kfreebsd-amd64 (unofficial port) 251.8 kB470 kB [list of files]
kfreebsd-i386 (unofficial port) 236.3 kB432 kB [list of files]
m68k 229.6 kB504 kB [list of files]
mips 257.4 kB608 kB [list of files]
mipsel 254.7 kB608 kB [list of files]
powerpc 254.5 kB568 kB [list of files]
s390 249.8 kB552 kB [list of files]
sparc 236.7 kB528 kB [list of files]