OCTOPUS Thursday, July 24 2014
Main Menu
Home
OCTOPUS
SPOCTOPUS
Download
Help
Download

The OCTOPUS software

For running large amounts of sequences a free for academic use standalone version of OCTOPUS (including SPOCTOPUS) is available for download. It is based on the gpl licensed software modhmm, a set of perl scripts, BLAST and PSI-BLAST. For it to compile and run the presence of among others gcc, perl, BLAST and PSI-BLAST is required. To build both modhmm and OCTOPUS, please refer to the TOPCONS suite of programs, available at www.topcons.net.

OCTOPUS training data

The data sets used to optimize and benchmark OCTOPUS:

readme
fasta.fa
topo.top
supplementary_fasta.fa
supplementary_topo.top
CROSSVAL_FILES.tar.gz

SPOCTOPUS predicted topologies

The data sets and predictions used in paper "SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology" by Viklund et al.:

ECOLI.TOP
YEAST.TOP
phobius.tar.gz

If you use these sets please refer to the original publications by Daley et al, 2005, Kim et al 2007 and Käll et al 2004.

 
 
© 2008 Stockholm University, Stockholm Bioinformatics Center