PMID: 9440929Jan 1, 1997Paper

Detection of eukaryotic promoters using Markov transition matrices

Computers & Chemistry
S Audic, J M Claverie

Abstract

Eukaryotic promoters are among the most important functional domains yet to be characterized in a satisfactory manner in genomic sequences. Most current detection methods rely on the recognition of individual transcription elements using position-weight matrices (PWM) or consensus sequences. Here, we study a simple promoter detection algorithm based on Markov transition matrices built from sequences upward from proven transcription initiation sites. The performances have been evaluated on the training set and on a test set of promoter-containing sequences. The results on the training set are surprisingly good, given that the algorithm does not incorporate any specific knowledge about promoters. Yet, the program exhibits the pathological behaviour typical of all training set-based methods: a significant decline in performance when confronted with previously unseen sequences. Thus, the Markov algorithm, like the others presently available, does not truly capture the essence of eukaryotic promoters. A detection program based on a Markov model is likely to be blind to categories of promoters without close representatives in the training set.

References

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Jan 1, 1997·Computers & Chemistry·J M ClaverieF Lopez

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Citations

Jan 1, 1997·Computers & Chemistry·J M ClaverieF Lopez
Jul 15, 1999·Computers & Chemistry·A G PedersenS Brunak
Dec 4, 2003·Bio Systems·Daniel Howard, Karl Benson
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gert ThijsYves Moreau
Mar 5, 2002·Genome Research·Thomas A Down, Tim J P Hubbard
Aug 26, 1998·Proceedings of the National Academy of Sciences of the United States of America·S Audic, J M Claverie
Apr 11, 2006·Journal of Theoretical Biology·Qian-Zhong Li, Hao Lin
Oct 21, 2005·Bio Systems·S P Pandey, A Krishnamachari
Jun 11, 1999·Current Opinion in Structural Biology·P Bucher
Aug 4, 2005·Artificial Intelligence in Medicine·Vipin NarangAnkush Mittal
Mar 31, 2004·Biotechnology and Bioengineering·Venugopal MikkilineniJeremy S Edwards
Oct 6, 1997·Genome Research·J W Fickett, A G Hatzigeorgiou
Sep 7, 2018·Molecular Genetics and Genomics : MGG·Md Siddiqur RahmanSwakkhar Shatabda

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