Review of : TRANSFAC - the transcription factor database

URL:                       http://transfac.gbf.de/TRANSFAC/index.html

Data reviewed:  TRANSFAC last updated 2001

                          Genomatix last updated 2002

Description: Program developed by a bioinformatics research group in Germany.  Focus is on sequence interpretation, namely of regulatory features for characterization of regulatory pathways and transcriptional networks.  Functional interpretation of sequences with regards to transcriptional importance, potential binding sites, and pattern search between sequences.

Strengths: Self explanatory instructions, easy to use, use defined searches, links to other programs for further analysis, additional databases available (MatInspector - search for potential transcription factor binding sites, FastM - generates matches for regulatory regions, PatSearch - pattern search for transcription factors, SaGa - analysis of aligned sequences for common structural characteristics); MatProfessional is my favorite prediction program here (you have to register for it); analysis of restriction sites possible

Weaknesses: sometimes the information one gets back for a sequence seems too much; maybe there should be one program that puts binding site analysis and comparison with known functional elements in one output file

Comprehensiveness: In my opinion it is a very complete program;

Timelines: very quick

Ease of Use: once one figured out how and for what the program can be utilized it is easy to use, very user friendly, easy to print

Responsiveness: Fast,

Similar or related sites: TRRD, Biomas at NIH, COMPEL

Overall Evaluation: ***** (5 stars)

Reviewer: Inka Pawlitzky (inka.pawlitzky@tufts.edu)