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

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 crea...

Full description

Saved in:

Bibliographic Details
Published in:	Bioinformatics Vol. 12; no. 5; pp. 441 - 446
Main Authors:	Karas, Holger, Knüppel, Rainer, Schulz, Wolfgang, Sklenar, Heinz, Wingender, Edgar
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-10-1996
Subjects:	Algorithms Base Sequence Binding Sites Databases, Factual DNA - analysis Models, Molecular Nucleic Acid Conformation Pattern Recognition, Automated Signal Transduction TATA Box Transcription, Genetic
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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
Bibliography:	istex:0404DE5597E68DD424D1746B5E3B9F1D03A110FB ark:/67375/HXZ-FPF5J1TK-M ArticleID:12.5.441 2To whom correspondence should be addressed
ISSN:	1367-4803 0266-7061 1460-2059
DOI:	10.1093/bioinformatics/12.5.441