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© Oxford University Press

Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements

Holger Karas , Rainer Knüppel , Wolfgang Schulz 1, Heinz Sklenar 1 and Edgar Wingender 2

Gesellschaft für Biotechnologische Forschung mbH Mascheroder Weg 1, D-38124 Braunschweig
1Max-Delbrück-Centrum für Molekulare Medizin Robert-Rössle-Str. 10, D-13125 Berlin-Buch, Germany

2To whom correspondence should be addressed

MOTIVATION: Analysis of unannotated genomic sequences for regulatory regions depends on a reliable recognition of individual cis-acting elements. Since some of them have a very low conserved sequence pattern, additional criteria are required.

RESULTS: Using molecular modelling techniques, we have created a complete database for the conversion of base sequences into profiles of structural parameters of DNA. On this basis, search routines can be developed that scan for profile matches. They may be used instead of or, probably most appropriate in most cases, in combination with conventional sequence pattern searches.

AVAILABILITY: The tools mentioned in the paper are available at {{http://transfac.gbf-braunschweig.de}}

CONTACT: e-mail: ewi{at}gbf.braunschweig.de


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