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CABIO,96,Karas
Combining structural analysis of DNA with search routines for
the detection of transcription regulatory elements
H. Karas, R. Knuppel, W. Schulz1,
H. sklenar1 and E. Wingender
Gesellschaft fur Biotechnologische Forschung mbH,
Mascheroder Weg 1, D-38124 Braunschweig,
Germany and
1Max-Delbruck-Centrum fur Molekulare Medizin, Robert-Rossle-Str.
10, D-13125 Berlin-Buch, Germany
Computer Applications in the Biosciences, 12(5), 441-446(Oct, 1996)
Abstract
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@gbf.braunschweig.de
