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[ Source: glam2  ]

Package: glam2 (1064-8 and others)

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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

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Download glam2

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha (unofficial port) 1064-8 234.6 kB558.0 kB [list of files]
amd64 1064-8 231.4 kB502.0 kB [list of files]
arm64 1064-8 224.7 kB494.0 kB [list of files]
armel 1064-8 217.7 kB469.0 kB [list of files]
armhf 1064-8 214.8 kB397.0 kB [list of files]
hppa (unofficial port) 1064-8 221.3 kB470.0 kB [list of files]
i386 1064-8 234.3 kB521.0 kB [list of files]
m68k (unofficial port) 1064-8 216.2 kB449.0 kB [list of files]
mips64el 1064-8 228.1 kB538.0 kB [list of files]
mipsel 1064-8 226.9 kB508.0 kB [list of files]
powerpcspe (unofficial port) 1064-7 221.0 kB625.0 kB [list of files]
ppc64 (unofficial port) 1064-8 239.0 kB758.0 kB [list of files]
ppc64el 1064-8 242.2 kB758.0 kB [list of files]
riscv64 (unofficial port) 1064-8 220.4 kB414.0 kB [list of files]
s390x 1064-8 227.4 kB510.0 kB [list of files]
sh4 (unofficial port) 1064-8 227.1 kB437.0 kB [list of files]
sparc64 (unofficial port) 1064-8 215.0 kB491.0 kB [list of files]
x32 (unofficial port) 1064-8 230.4 kB489.0 kB [list of files]