PMID: 8590170Oct 1, 1995Paper

Eukaryotic promoter recognition by binding sites for transcription factors

Computer Applications in the Biosciences : CABIOS
Y V KondrakhinL Milanesi

Abstract

A method for identification of eukaryotic promoters by localization of binding sites for transcription factors has been suggested. The binding sites for a range of transcription factors have been found to be distributed unevenly. Based on these distributions, we have constructed a weight matrix of binding site localization. On the basis of the weight matrix we have, in turn, designed an algorithm for promoter recognition. To increase the accuracy of the method, we have developed a routine that breaks any promoter sample into subsamples. The method to be reported on allows much better recognition accuracy than does the approach based on detection of the TATA box. In particular, the overprediction error is three times lower following our method. The program FunSiteP recognizes promoters from newly uncovered sequences and tentatively identifies the functional class the promoters must belong to. We have introduced the notion of 'regulatory potential' for the degree to which any region of the sequences is similar to the real eukaryotic promoter. By making use of the potential, we have revealed putative transcription start sites and extended regions of transcription regulation.

Citations

Jan 1, 2010·Biological Procedures Online·Yu-Ling LinKuang-Wen Liao
Sep 1, 1996·The International Journal of Biochemistry & Cell Biology·D S Latchman
Oct 1, 1996·The International Journal of Biochemistry & Cell Biology·D S Latchman
Jul 15, 1999·Computers & Chemistry·A G PedersenS Brunak
Jan 19, 2000·Neurobiology of Aging·L G HarshmanM M Magwire
Nov 26, 1999·Gene·G Suske
Mar 14, 2000·Gene·V FilippovS S Gill
Feb 15, 2000·Research in Microbiology·A VanetM F Sagot
Jun 1, 1997·Current Opinion in Structural Biology·L Duret, P Bucher
May 7, 1998·The International Journal of Biochemistry & Cell Biology·D S Latchman
Dec 1, 1996·Nucleic Acids Research·J KleffeV Brendel
Jun 26, 2003·Nucleic Acids Research·Martin C FrithZhiping Weng
Jun 28, 2005·Nucleic Acids Research·Oleg V Vishnevsky, Nikolay A Kolchanov
Apr 3, 2003·Genome Research·Alexander P LifanovDmitri A Papatsenko
Jul 15, 2003·Plant Physiology·Stephane RombautsYves van de Peer
Jan 28, 1998·Annual Review of Entomology·L G Harshman, A A James
Jan 14, 2005·Theoretical Biology & Medical Modelling·Ekaterina Shelest, Edgar Wingender
Aug 4, 2005·Artificial Intelligence in Medicine·Vipin NarangAnkush Mittal
Nov 16, 2017·PloS One·Martin TriskaTatiana V Tatarinova
Oct 6, 1997·Genome Research·J W Fickett, A G Hatzigeorgiou

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