Re: Debian package for MEME motif search available
On Thu, 20 Jan 2005, Steffen Moeller wrote:
I created a first Debian package for MEME. The tool is well known in the
community. It has some drawbacks like that it differnetially find
patterns that are only in one set of sequences but not in another (SPEXS
can do that) but it is well accepted in the community.
When browsing my mailbox I just found your mail probably unanswered.
It is available (as usual) at
http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/meme
I'd be happy for anybody to jump in to write the man pages, separate the
website to an extra package and maybe even prepare the MPI-based parallel
binaries in yet another package. So - while of interest to the community
the package is not yet ready for being sponsored, I am afraid.
I agree with the last part from a "lintian-point-of-view".
Besides the debian/*.ex examples the package seems to be full of csh
code. Porting each single script to POSIX would be a lot of work and
I would not like to do that if upstream does not agree here. So we
might add a dependency tcsh | csh to fix this.
Description: [Biology] search for common motifs in DNA or protein
sequences
MEME (Multiple EM for Motif Elicitation) discovers motifs in sequences.
.
A motif is a sequence pattern that occurs repeatedly in a group
of related protein or DNA sequences. Motifs are represented as
position-dependent scoring matrices that describe the score of each
possible letter at each position in the pattern. Individual motifs may
not contain gaps but combinations of patterns may be elucidated.
.
The output of MEME may be forwarded to the program MAST of this package
for the search in sequence databases.
.
Homepage: http://meme.sdsc.edu
Anybody wants to step in to continue the work of Steffen?
Kind regards
Andreas.
--
http://fam-tille.de
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