Difference between revisions of "Tools for matrices"

From OpenWetWare
Jump to: navigation, search
(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 ...)
 
 
Line 1: Line 1:
 
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
** Enologo: Some advantages over weblogo, can plot matrices
+
** [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

Latest revision as of 04:26, 4 March 2008

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