Software
Purpose
Link
COMPASS
Protein threading/fold recognition
http://prodata.swmed.edu/compass/compass.php
CS/CSI-BLAST
Protein threading/fold recognition
http://toolkit.tuebingen.mpg.de/cs_blast
HHpred
Protein threading/fold recognition
http://toolkit.tuebingen.mpg.de/hhpred
HMMER
Protein threading/fold recognition
http://hmmer.janelia.org
NCBI BLAST
Sequence alignment
http://blast.ncbi.nlm.nih.gov/Blast.cgi
pfTools
Protein threading/fold and motif recognition
ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/README
pGenThreader
Protein threading/fold recognition
http://bioinf.cs.ucl.ac.uk/psipred/?program=mgenthreader
PSIPRED
Secondary structure prediction
http://bioinf.cs.ucl.ac.uk/psipred
SAM-T2K
Protein threading/fold recognition
http://compbio.soe.ucsc.edu/papers/sam_doc/sam_doc.html
SPARKS/SP3
Protein threading/fold recognition
http://sparks.informatics.iupui.edu/index.php?pageLoc=Services
Threader
Protein threading/fold recognition
http://bioinf.cs.ucl.ac.uk/software_downloads/threader
Table 1:
Sequence-based tools. Components of the eThread pipeline for protein threading and sequence analysis.