Literature DB >> 11836231

Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters.

Vladimir B Bajic1, Seng Hong Seah, Allen Chong, Guanglan Zhang, Judice L Y Koh, Vladimir Brusic.   

Abstract

Dragon Promoter Finder (DPF) locates RNA polymerase II promoters in DNA sequences of vertebrates by predicting Transcription Start Site (TSS) positions. DPF's algorithm uses sensors for three functional regions (promoters, exons and introns) and an Artificial Neural Network (ANN). Results on a large and diverse evaluation set indicate that DPF exhibits a superior predicting ability for TSS location compared to three other promoter-finding programs.

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Year:  2002        PMID： 11836231     DOI： 10.1093/bioinformatics/18.1.198

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  36 in total

1.  Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes.

Authors:  Vladimir B Bajic; Sin Lam Tan; Allen Chong; Suisheng Tang; Anders Ström; Jan-Ake Gustafsson; Chin-Yo Lin; Edison T Liu
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes.

Authors:  Allen Chong; Guanglan Zhang; Vladimir B Bajic
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  PromH: Promoters identification using orthologous genomic sequences.

Authors:  V V Solovyev; I A Shahmuradov
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 4.  Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Authors:  Stephane Rombauts; Kobe Florquin; Magali Lescot; Kathleen Marchal; Pierre Rouzé; Yves van de Peer
Journal:  Plant Physiol       Date:  2003-07       Impact factor: 8.340

5.  Generic eukaryotic core promoter prediction using structural features of DNA.

Authors:  Thomas Abeel; Yvan Saeys; Eric Bonnet; Pierre Rouzé; Yves Van de Peer
Journal:  Genome Res       Date:  2007-12-20       Impact factor: 9.043

6.  A transcription factor affinity-based code for mammalian transcription initiation.

Authors:  Molly Megraw; Fernando Pereira; Shane T Jensen; Uwe Ohler; Artemis G Hatzigeorgiou
Journal:  Genome Res       Date:  2009-01-13       Impact factor: 9.043

7.  High-resolution human core-promoter prediction with CoreBoost_HM.

Authors:  Xiaowo Wang; Zhenyu Xuan; Xiaoyue Zhao; Yanda Li; Michael Q Zhang
Journal:  Genome Res       Date:  2008-11-07       Impact factor: 9.043

8.  Eukaryotic and prokaryotic promoter prediction using hybrid approach.

Authors:  Hao Lin; Qian-Zhong Li
Journal:  Theory Biosci       Date:  2010-11-03       Impact factor: 1.919

9.  Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units.

Authors:  Vladimir B Bajic; Seng Hong Seah
Journal:  Genome Res       Date:  2003-07-17       Impact factor: 9.043

10.  ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.

Authors:  Thomas Abeel; Yvan Saeys; Pierre Rouzé; Yves Van de Peer
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937
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