MOTIVATION: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. RESULTS: We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
MOTIVATION: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. RESULTS: We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
Authors: Yanxia Ning; Rebecca B Riggins; Jennifer E Mulla; Haniee Chung; Alan Zwart; Robert Clarke Journal: Mol Cancer Ther Date: 2010-05 Impact factor: 6.261
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Authors: Clemens D Cohen; Andreas Klingenhoff; Anissa Boucherot; Almut Nitsche; Anna Henger; Bodo Brunner; Holger Schmid; Monika Merkle; Moin A Saleem; Klaus-Peter Koller; Thomas Werner; Hermann-Josef Gröne; Peter J Nelson; Matthias Kretzler Journal: Proc Natl Acad Sci U S A Date: 2006-03-31 Impact factor: 11.205
Authors: D Tuñón-Le Poultel; J B Cannata-Andía; P Román-García; J B Díaz-López; E Coto; C Gómez; M Naves-Díaz; I Rodríguez Journal: Osteoporos Int Date: 2013-11-27 Impact factor: 4.507