Hello,
I just read an announcement of the GMOD workshop in San Diego (January,
2012) http://www.intl-pag.org/19/19-gmod.html featuring a session on
MAKER http://gmod.org/wiki/MAKER , their genome annotation environment.
This environment might be an excellent opportunity to interlink our
current (!) packages more. From their requirements list:
* Perl 5.8.0 or higher
* BioPerl <http://gmod.org/wiki/BioPerl> 1.6 or higher.
* WU-BLAST <http://blast.wustl.edu> 2.0 or higher or NCBI-BLAST
<http://www.ncbi.nlm.nih.gov/> 2.2.X or higher
* SNAP <http://homepage.mac.com/iankorf> version 2009-02-03 or
higher (for eukaryotic genomes).
* RepeatMasker <http://www.repeatmasker.org/> 3.1.6 or higher
o RepeatMasker requires a repeat library, available from
Repbase <http://www.girinst.org/repbase/index.html>.
* Exonerate <http://www.ebi.ac.uk/%7Eguy/exonerate> 1.4 or higher.
So, exonerate we have, bioperl we have - Olivier pointed out that it
needs to be updated, blast is there. SNAP is missing and a bit to my
surprise we don't have RepeatMasker. There is another crowd of
additional further gene predictors suggested. Well, time is limited.
Interesting, and maybe challenging, RepeatMasker demands to got with a
database that is separated from the binary.
Many greetings
Steffen
