Biosquid, HMMER and an update to microbio.wml
Hi people!
Andreas Tille kindly uploaded a new package: biosquid [1], a set of
utilities for biological sequence analysis.
It's on the NEW queue [2] now, waiting for the FTP-masters approval.
The package description is:
SQUID is a library of C code functions for sequence analysis. It also
includes a number of small utility programs to convert, show
statistics, manipulate and do other functions on sequence files.
The original name of the package is "squid", but since there is
already a squid on the archive (a proxy cache), it was renamed to
"biosquid".
[1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=319945
[2] http://ftp-master.debian.org/new.html
Also, I have talked with Matthew Vernon and he allowed me to update
Hmmer on Debian. A new version of Hmmer will enter Debian soon.
Tobias, I am CCing you to see if you could updated microbio.wml, please.
I have attached a patch, including the new biosquid and also a small
update of Hmmer.
Thank you very much!
Cheers,
Nelson
--- microbio.wml.old 2006-08-07 00:59:13.000000000 -0300
+++ microbio.wml 2006-08-07 01:30:27.000000000 -0300
@@ -51,6 +51,22 @@
</project>
+<project name="BioSQUID"
+ url="http://selab.wustl.edu/cgi-bin/selab.pl?mode=software";
+ license="GPL"
+ deb="http://packages.debian.org/unstable/science/biosquid";>
+ <p>
+ BioSQUID is a library of C code functions for sequence analysis. It also
+ includes a number of small utility programs to convert, show statistics,
+ manipulate and do other functions on sequence files.
+ </p>
+ <p>
+ Originally known as SQUID it was renamed to BioSQUID, as suggested by
+ the upstream author Sean Eddy.
+ </p>
+</project>
+
+
<project name="BLAST2"
url="http://www.ncbi.nlm.nih.gov/BLAST/";
license="<free />"
@@ -229,9 +245,17 @@
url="http://hmmer.wustl.edu/";
license="GPL"
deb="http://packages.debian.org/unstable/science/hmmer";>
- Hmmer is a suite of programs which use profile hidden Markov models
- (profile HMMs) to model the primary structure consensus of a family
- of protein or nucleic acid sequences.
+ <p>
+ HMMER is an implementation of profile hidden Markov model methods for
+ sensitive searches of biological sequence databases using multiple sequence
+ alignments as queries.
+ </p>
+ <p>
+ Given a multiple sequence alignment as input, HMMER builds a statistical
+ model called a "hidden Markov model" which can then be used as a query into
+ a sequence database to find (and/or align) additional homologues of the
+ sequence family.
+ </p>
</project>
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