Tools for matrices
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(Difference between revisions)
(New page: Once you have found some known binding sites: * Plot them: ** Delila tools: Old but not very usable ** Weblogo: The best tool on the web to generate logos ** Enologo: Some advantages over ...) |
Current revision (08:26, 4 March 2008) (view source) |
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Once you have found some known binding sites: | Once you have found some known binding sites: | ||
* Plot them: | * Plot them: | ||
| - | ** Delila tools: Old but not very usable | + | ** [http://www.ccrnp.ncifcrf.gov/~toms/logoprograms.html Delila tools]: Old but not very usable. I suggest you avoid them. |
| - | ** Weblogo: The best tool on the web to generate logos | + | ** [http://weblogo.berkeley.edu/ Weblogo]: The best tool on the web to generate logos |
| - | ** | + | ** [http://biodev.hgen.pitt.edu/cgi-bin/enologos/enologos.cgi Enologos]: Some advantages over weblogo, can plot matrices, but not in transfac format |
* Compare them: | * Compare them: | ||
| + | ** [http://treg.molgen.mpg.de/cgi-bin/pfm_meme_form.pl T-Reg comparator]: Compares against your motifs or an internal database of Transfac+Jaspar | ||
| + | ** [http://atlas.med.harvard.edu/cgi-bin/compareace.pl CompareACE] as part of AlignACE | ||
| + | ** [http://rulai.cshl.edu/MatCompare/ MatCompare]: As part of CREAD | ||
Current revision
Once you have found some known binding sites:
- Plot them:
- Delila tools: Old but not very usable. I suggest you avoid them.
- Weblogo: The best tool on the web to generate logos
- Enologos: Some advantages over weblogo, can plot matrices, but not in transfac format
- Compare them:
- T-Reg comparator: Compares against your motifs or an internal database of Transfac+Jaspar
- CompareACE as part of AlignACE
- MatCompare: As part of CREAD
