Literature DB >> 19812788

IMAGE: a new tool for the prediction of transcription factor binding sites.

R Casilli1, A Marongiu, S Melchionna, P Palazzari, R Paparcone, V Rosato.   

Abstract

IMAGE is an application tool, based on the vector quantization method, aiding the discovery of nucleotidic sequences corresponding to Transcription Factor binding sites. Starting from the knowledge of regulation regions of a number of co-expressed genes, the software is able to predict the occurrence of specific motifs of different lengths (starting from 6 base pairs) with a defined number of punctual mutations.

Entities:  

Year:  2008        PMID： 19812788      PMCID： PMC2735968     

Source DB:  PubMed          Journal:  Bioinform Biol Insights        ISSN： 1177-9322


  10 in total

Review 1.  DNA binding sites: representation and discovery.

Authors:  G D Stormo
Journal:  Bioinformatics       Date:  2000-01       Impact factor: 6.937

2.  Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.

Authors:  L Marsan; M F Sagot
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

3.  Identifying target sites for cooperatively binding factors.

Authors:  D GuhaThakurta; G D Stormo
Journal:  Bioinformatics       Date:  2001-07       Impact factor: 6.937

4.  A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

Authors:  G Thijs; M Lescot; K Marchal; S Rombauts; B De Moor; P Rouzé; Y Moreau
Journal:  Bioinformatics       Date:  2001-12       Impact factor: 6.937

5.  Finding functional sequence elements by multiple local alignment.

Authors:  Martin C Frith; Ulla Hansen; John L Spouge; Zhiping Weng
Journal:  Nucleic Acids Res       Date:  2004-01-02       Impact factor: 16.971

6.  Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.

Authors:  Giulio Pavesi; Paolo Mereghetti; Giancarlo Mauri; Graziano Pesole
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  Discovery of regulatory elements in vertebrates through comparative genomics.

Authors:  Amol Prakash; Martin Tompa
Journal:  Nat Biotechnol       Date:  2005-10       Impact factor: 54.908

8.  Evaluation of gene structure prediction programs.

Authors:  M Burset; R Guigó
Journal:  Genomics       Date:  1996-06-15       Impact factor: 5.736

9.  Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

Authors:  C E Lawrence; S F Altschul; M S Boguski; J S Liu; A F Neuwald; J C Wootton
Journal:  Science       Date:  1993-10-08       Impact factor: 47.728

10.  Assessing computational tools for the discovery of transcription factor binding sites.

Authors:  Martin Tompa; Nan Li; Timothy L Bailey; George M Church; Bart De Moor; Eleazar Eskin; Alexander V Favorov; Martin C Frith; Yutao Fu; W James Kent; Vsevolod J Makeev; Andrei A Mironov; William Stafford Noble; Giulio Pavesi; Graziano Pesole; Mireille Régnier; Nicolas Simonis; Saurabh Sinha; Gert Thijs; Jacques van Helden; Mathias Vandenbogaert; Zhiping Weng; Christopher Workman; Chun Ye; Zhou Zhu
Journal:  Nat Biotechnol       Date:  2005-01       Impact factor: 54.908
  10 in total

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