Table 2.
Summary of motif discovery and motif scanning tools. The addresses link to the author's website
| Tool | Web site | Reference |
|---|---|---|
| Motif Discovery—single sequence output | ||
| BioProspector | http://ai.stanford.edu/~xsliu/BioProspector/ | (33) |
| DME | http://rulai.cshl.edu/dme/index.shtml | (34) |
| GAME | http://mail.med.upenn.edu/~zhiwei/GAME/ | (35) |
| nMICA | http://www.sanger.ac.uk/Software/analysis/nmica/ | (36) |
| Weeder | http://159.149.109.16:8080/weederWeb/ | (37) |
| YMF | http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl | (38) |
| Motif Discovery—orthologous sequence output | ||
| PhyloCon | http://ural.wustl.edu/~twang/PhyloCon/ | (39) |
| PhyloGibbs | http://www.imsc.res.in/~rsidd/phylogibbs/ http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl | (40) |
| PhyME | http://edsc.rockefeller.edu/cgi-bin/phyme/download.pl | (41) |
| MotifScanning | ||
| Clover | http://biowulf.bu.edu/MotifViz/ | (42) |
| MotifScanner | http://homes.esat.kuleuven.be/~thijs/Work/MotifScanner.html | Unpublished |
| PROMO | http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promo.cgi?dirDB=TF_8.3&calledBy=alggen | (43,44) |