Treffer: Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity

Title:
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
Authors:
KLINGENHOFF, A, FRECH, K, QUANDT, K, WERNER, T
Source:
Selection of papers presented at the German Conference on Bioinformatics (GCB'98, Cologne, Germany, October 1998Bioinformatics (Oxford. Print). 15(3):180-186
Publisher Information:
Oxford: Oxford University Press, 1999.
Publication Year:
1999
Physical Description:
print, 27 ref
Original Material:
INIST-CNRS
Subject Terms:
Bioinformatics, Bioinformatique, Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Generalites, General aspects, Mathématiques biologiques. Statistiques. Modèles. Métrologie. Informatique en biologie (généralités), Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects), Traitement informatique, Computerized processing, Tratamiento informático, Détection, Detection, Detección, Etude comparative, Comparative study, Estudio comparativo, Logiciel, Software, Logicial, Modèle, Models, Modelo, Méthode, Method, Método, Promoteur transcription, Transcription promoter, Promotor transcripción, Séquence nucléotide, Nucleotide sequence, Secuencia nucleótido
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Institute of Mammalian Genetics, GSF-National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
Genomatix Software GmbH, Karlstrasse 55, 80333 Munchen, Germany
ISSN:
1367-4803
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=1831434
Rights:
Copyright 1999 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Biological sciences. Generalities. Modelling. Methods

Generalities in biological sciences
Accession Number:
edscal.1831434
Database:
PASCAL Archive

Weitere Informationen

Motivation: Gene regulation often depends on functional modules which feature a detectable internal organization. Overall sequence similarity of these modules is often insufficient for detection by general search methods like FASTA or even Gapped BLAST. However it is of interest to evaluate whether modules, often known from experimental analysis of single sequences, are present in other regulatory sequences. Results: We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (Matlnspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites derived from as little as a single promoter or enhancer Modellnspector results are suitable for evaluation of the significance of the model. We used FastM to define a model for the experimentally verified NFκB/IRF1 regulatory module from the major histocompatibility complex (MHC) class I HLA-B gene promoter Analysis of a test set of sequences as well as database searches with this model showed excellent correlation ofthe model with the biological function of the module. These results could not be obtained by searches using FASTA or Gapped BLAST, which are based on sequence similarity. We were also able to demonstrate association of hypothetical GRE-GRE module with viral sequences based on analysis of several GenBank sections with this module.