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. Author manuscript; available in PMC: 2015 May 27.
Published in final edited form as: Methods Enzymol. 2007;422:47–74. doi: 10.1016/S0076-6879(06)22003-2

Table 2.

Computational resources for prediction of signal peptides and transmembrane segments in proteins

Name URL No. of sequences Reference
Prediction of signal peptides
SignalP http://www.cbs.dtu.dk/services/SignalP ≤ 2000 Bendtsen et al., 2004
LipoP http://www.cbs.dtu.dk/services/LipoP/ ≤ 4000 Juncker et al., 2003
PSORT http://www.psort.org/ ≤ 2000a Gardy et al., 2005
SOSUI signal http://harrier.nagahama-i-bio.ac.jp/sosui/sosuisignal/sosuisignal_submit.html 1 Gomi et al., 2004
Prediction of transmembrane segments
TMHMM http://www.cbs.dtu.dk/services/TMHMM/ ≤ 4000 Krogh et al., 2001
ConPred http://bioinfo.si.hirosaki-u.ac.jp/%7EConPred2/ ≤ 100 Arai et al., 2004
DAS http://mendel.imp.ac.at/sat/DAS/DAS.html ≤ 50 Cserzo et al., 2004
HMMTOP http://www.enzim.hu/hmmtop/ N/Aa Tusnady and Simon, 2001
MEMSAT http://bioinf.cs.ucl.ac.uk/psipred/ 1 Jones et al., 1994
Phobius http://phobius.cgb.ki.se/ 1 Kall et al., 2004
PSORT http://www.psort.org/ ≤ 2000a Gardy et al., 2005
SOSUI http://bp.nuap.nagoya-u.ac.jp/sosui/ N/Aa Hirokawa et al., 1998
SVMtm http://ccb.imb.uq.edu.au/svmtm/ ≤ 25a Yuan et al., 2004
TMpred http://www.ch.embnet.org/software/TMPRED_form.html 1 Hofmann and Stoffel, 1993
TMAP http://bioweb.pasteur.fr/seqanal/interfaces/tmap.html 1 Persson and Argos, 1997
TopPred http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html 1 Claros and von Heijne, 1994
a

The actual limitation for PSORT is 600,000 characters, for SVMtm - 10 KB; N/A means that the server accept multiple sequences but the exact limit is not specified.