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.
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