Matlnspector and beyond: promoter analysis based on transcription factor binding sites

被引：1658

作者：

Cartharius, K ^{[1
]}

Frech, K ^{[1
]}

Grote, K ^{[1
]}

Klocke, B ^{[1
]}

Haltmeier, M ^{[1
]}

Klingenhoff, A ^{[1
]}

Frisch, M ^{[1
]}

Bayerlein, M ^{[1
]}

Werner, T ^{[1
]}

机构：

[1] Genomatix Software GmbH, D-80339 Munich, Germany

来源：

BIOINFORMATICS | 2005年 / 21卷 / 13期

关键词：

D O I：

10.1093/bioinformatics/bti473

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 nucleoticle 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). Availability: MatInspector and the other programs described here can be used online at http://www.genomatix.de/matinspector.html. Access is free after registration within certain limitations (e.g. the number of analysis per month is currently limited to 20 analyses of arbitrary sequences).

引用

页码：2933 / 2942

页数：10

共 49 条

[1] Rat osteoblast and osteosarcoma nuclear matrix proteins bind with sequence specificity to the rat type I collagen promoter [J].