Table VI.
Programs used for sequence analysis and targeting prediction cTP, Chloroplast targeting peptide; mTP, mitochondrial targeting peptide; NLS, nuclear localization signal; TMH, transmembrane helix; SP, signal peptide (ER, secretory pathway).
| Program | Predicted Feature | URL | Reference |
|---|---|---|---|
| MultiCoil 1.0 | Coiled-coil | http://theory.lcs.mit.edu/multicoil | Wolf et al. (1997) |
| ChloroP 1.1 | cTP | http://www.cbs.dtu.dk/services/ChloroP/ | Emanuelsson et al. (1999) |
| Predotar 0.5 | cTP, mTP | http://www.inra.fr/predotar/ | |
| TargetP 1.01 | cTP, mTP, SP, other | http://www.cbs.dtu.dk/services/TargetP/ | Nielsen et al. (1997a), Emanuelsson et al. (2000) |
| MitoProt II | mTP | http://www.mips.biochem.mpg.de/cgi-bin/proj/mcdgcn/mitofilter | Claros et al. (1996) |
| PredictNLS | NLS | http://maple.bioc.columbia.edu/predictNLS/ | Cokol et al. (2000) |
| PSORT | NLS, TMH | http://psort.nibb.ac.jp/ | Nakai and Horton (1999) |
| SignalP 2.0 HMM | SP | http://www.cbs.dtu.dk/services/SignalP-2.0/ | Nielsen and Krogh (1998) |
| SignalP 2.0 NN | SP | http://www.cbs.dtu.dk/services/SignalP-2.0/ | Nielsen et al. (1997b) |
| TMHMM 2.0 | TMH | http://www.cbs.dtu.dk/services/TMHMM/ | Sonnhammer et al. (1998), Krogh et al. (2001) |
| HMMTOP1.1 | TMH | http://www.enzim.hu/hmmtop/ | Tusnády and Simon (1998) |
| Several | TMH | http://aramemnon.botanik.uni-koeln.dc | Schwacke et al. (2003) |