PROMO HOME PAGE

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files.

PROMO is using version 8.3 of TRANSFAC.

If you use the results in your research please cite:

Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Nuñez, Javier Martínez, M.Mar Albà. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics, 18, 2, 333-334, 2002.

Domènec Farré, Romà Roset, Mario Huerta, José E. Adsuara, Llorenç Roselló, M.Mar Albà, Xavier Messeguer. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res, 31, 13, 3651-3653, 2003.

Search for putative sites in your sequence:

step 1.

SelectSpecies: select the species or group of species of interest.

      Current factor's species or group: All species
      Current site's species or group: All species

Also you can SelectFactors to restrict the prediction to a transcription factor set.

step 2.

SearchSites: input a query sequence to search for potential binding sites

or MultiSearchSites:input a set of sequences to search for binding sites that different sequences share.
 

Other tools:
ViewMatrices:view details on weight matrices being used.
 
More information:
See help . 
Links to other programs and databases
The supervisor of this site is D. Farré.

PEOPLE

This is a collaborative research project between Dr. M.M. Albà and D. Farré at the Evolutionary Genomics Group (Research Unit on Biomedical Informatics, Universitat Pompeu Fabra) and D. García, R. Escudero, O. Nuñez, J. Martínez and Dr. X. Messeguer of the Universitat Politècnica de Catalunya.

This site is partially supported by project DGES PB98-0926 (AEDRI; Algorithms and Data Structures for Information Retrieval)


Version 3.0.2