Package: glam2 (1064-9 and others)

[ 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.

This package includes programs for discovering motifs shared by a set of sequences and finding matches to these motifs in a sequence database, as well as utilities for converting glam2 motifs to standard alignment formats, masking glam2 motifs out of sequences so that weaker motifs can be found, and removing highly similar members of a set of sequences.

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 binary package, the fast Fourier algorithm (FFT) was enabled for the glam2 program.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c, interface::commandline, Role: Program, Scope: Utility, Purpose: use::analysing, use::comparing, Searching, Supports Format: works-with-format::TODO, works-with-format::plaintext, Works with: Need an extra tag

Other Packages Related to glam2

• dep: libc6 (>= 2.29) [not alpha, ia64, riscv64, sh4]

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

  dep: libc6 (>= 2.31) [sh4]

  dep: libc6 (>= 2.34) [riscv64]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.31) [ia64]

• dep: libfftw3-double3 (>= 3.3.10) [riscv64]

  Library for computing Fast Fourier Transforms - Double precision

  dep: libfftw3-double3 (>= 3.3.5) [not riscv64]

Download glam2

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1064-9	232.9 kB	555.0 kB	[list of files]
amd64	1064-9	230.0 kB	507.0 kB	[list of files]
arm64	1064-9	222.7 kB	491.0 kB	[list of files]
armel	1064-9	216.8 kB	474.0 kB	[list of files]
armhf	1064-9	214.4 kB	402.0 kB	[list of files]
hppa (unofficial port)	1064-9	220.8 kB	475.0 kB	[list of files]
i386	1064-9	233.3 kB	518.0 kB	[list of files]
ia64 (unofficial port)	1064-9	250.9 kB	717.0 kB	[list of files]
m68k (unofficial port)	1064-9	214.9 kB	454.0 kB	[list of files]
mips64el	1064-9	227.4 kB	543.0 kB	[list of files]
ppc64 (unofficial port)	1064-9	239.7 kB	763.0 kB	[list of files]
ppc64el	1064-9	242.6 kB	763.0 kB	[list of files]
riscv64	1064-9+b1	231.2 kB	454.0 kB	[list of files]
s390x	1064-9	226.3 kB	515.0 kB	[list of files]
sh4 (unofficial port)	1064-9	226.3 kB	438.0 kB	[list of files]
sparc64 (unofficial port)	1064-9	213.9 kB	488.0 kB	[list of files]
x32 (unofficial port)	1064-9	229.2 kB	490.0 kB	[list of files]