This distribution contains code common to Bioinformatics-related developement in the SBG (Structural Bioinformatics Group) of Prof. Rob Russell
DOCUMENTATION
Run:
perldoc ./lib/SBG.pm perldoc ./lib/SBG/Tutorial.pm
Also see the examples in ./examples/ and the tests in ./t/
DEPENDENCIES
STAMP (stamp, pdbc, pdbseq, transform, cofm)
PDL requires manual installation until the 2.4.10 version is released.
cpan install CHM/PDL-2.4.10.tar.gz
install CHM/PDL-2.4.9_009.tar.gz
Other requirements can be installed via APT (on Debian/Ubuntu)
Optional:
INSTALLATION
perl Makefile.PL make # Will install any other module dependencies make test make install
PROTEIN DATA BANK (PDB)
To download PDB files, use the tools provided with STAMP: http://code.google.com/p/bio-stamp/source/browse/trunk/README
BLAST DATABASES
The NCBI pdbaa Blast database does not include aliases for all sequences when they are 100% identical. We provide a script to retain these aliases. Note, sequences are not duplicated in the Blast databases, only the aliases are tracked.
export BLASTDB=/usr/local/data/blastdb mkdir -p $BLASTDB cd $BLASTDB
sbg-update-blastdb.pl [ pdbaa ]
The 'pdbseq' database : (Sequences based on C-alpha atoms from structure). See the instructions provided by STAMP:
http://code.google.com/p/bio-stamp/source/browse/trunk/README
HOME PAGE
BUGS
http://code.google.com/p/sbglib/issues/list
COPYRIGHT AND LICENCE
Copyright (C) 2007-2011 Chad A Davis chad.a.davis@gmail.com
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.