Package: glam2 (1064-1)

[ Source: glam2  ]

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).

Tags: Field: Biology, Bioinformatics, Implemented in: C, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Analysing, Comparing, Searching, Supports Format: Plain Text

Other Packages Related to glam2

• dep: libc0.1 (>= 2.3) [kfreebsd-amd64, kfreebsd-i386]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc0.1-udeb

• dep: libc0.3 (>= 2.7-1) [hurd-i386]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc0.3-udeb

• dep: libc6 (>= 2.11) [powerpcspe]

  Embedded GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.13) [s390x]

  dep: libc6 (>= 2.5) [avr32]

  dep: libc6 (>= 2.5-5) [m68k]

  dep: libc6 (>= 2.7) [armhf, sparc64]

  dep: libc6 (>= 2.7-1) [amd64, armel, hppa, i386, mips, mipsel, powerpc, s390, sparc]

  dep: libc6 (>= 2.9) [sh4]

• dep: libc6.1 (>= 2.7-1) [alpha, ia64]

  Embedded 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 kB	616.0 kB	[list of files]
amd64	251.9 kB	548.0 kB	[list of files]
armel	246.5 kB	536.0 kB	[list of files]
armhf	232.4 kB	377.0 kB	[list of files]
avr32 (unofficial port)	232.1 kB	476.0 kB	[list of files]
hppa	255.7 kB	556.0 kB	[list of files]
hurd-i386	235.0 kB	508.0 kB	[list of files]
i386	234.8 kB	460.0 kB	[list of files]
ia64	307.0 kB	756.0 kB	[list of files]
kfreebsd-amd64	249.6 kB	464.0 kB	[list of files]
kfreebsd-i386	235.7 kB	428.0 kB	[list of files]
m68k (unofficial port)	229.6 kB	504.0 kB	[list of files]
mips	257.4 kB	608.0 kB	[list of files]
mipsel	254.7 kB	608.0 kB	[list of files]
powerpc	254.5 kB	568.0 kB	[list of files]
powerpcspe (unofficial port)	254.2 kB	540.0 kB	[list of files]
s390	249.8 kB	552.0 kB	[list of files]
s390x	263.5 kB	482.0 kB	[list of files]
sh4 (unofficial port)	251.3 kB	528.0 kB	[list of files]
sparc	236.7 kB	528.0 kB	[list of files]
sparc64 (unofficial port)	243.9 kB	548.0 kB	[list of files]