FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

被引：17

作者：

Corcoran, DL

Feingold, E

Benos, PV ^{[1
]}

机构：

[1] Univ Pittsburgh, Grad Sch Publ Hlth, Dept Human Genet, Pittsburgh, PA 15260 USA

[2] Univ Pittsburgh, Grad Sch Publ Hlth, Dept Biostat, Pittsburgh, PA USA

[3] Univ Pittsburgh, Dept Computat Biol, Pittsburgh, PA USA

[4] Univ Pittsburgh, Sch Med, Inst Canc, Pittsburgh, PA USA

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/nar/gki420

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory 'signals'. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at http://biodev.hgen.pitt.edu/Footer/.

引用

页码：W442 / W446

页数：5

共 25 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].