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.