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TESS 1.0
Introduction
TESS (Transcription Element Search Software) is a set of software for locating and displaying transcription factor binding sites in DNA sequence. TESS uses the Transfac database as its store of transcription factors and their binding sites.
Features
Web-browsable version of Transfac
A browser which will let the user look and search the entries in Transfac for keywords and view the results in various formats.
String-Based Search
This search will look for matches between substrings of your sequence and sequences listed in the SITES table in the Transfac database. The user can specify the level of mismatch to accept. Results are presented in both graphical and tabulated form.
More information about matching factors can be easily retrieved using hot links to our Transfac browser.
This search is the slower of the two but is more complete.
Filtered String-Based Search
This search is the same as the string search above but the user has the additional ability to limit the factors used in the search. This is done using pattern matching on a selected attribute. Using this feature the factors can be limited by species, classification, expression pattern, cell line, class, etc. A table of the factors used in the search is displayed at the end of the results page.
This will allow more rapid searching when not all factors are of interest.
Weight-Matrix-Based Search
This search will look for matches between substrings of your sequence and weight matrices listed in the MATRIX table of the Transfac database. The user can specify the level of mismatch to accept. Results are presented in both graphical and tabulated form.. More information about matching factors can be easily retrieved using hot links to the Transfac browser.
This search is the fastest of the two but only identifies factors that have a weight matrix model of a binding site.
Information provided by: Jonathan Schug
Resources and further information
University of Pennsylvania
http://www.upenn.edu/
Computational Biology and Informatics Laboratory
http://www.cbil.upenn.edu/
TESS homepage
http://agave.humgen.upenn.edu/utess/tess/
TRANSFAC information (elsewhere in this issue)
http://bioinformer.ebi.ac.uk/newsletter/archives/2/TRANSFAC32_lon g.html
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