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>
