Article (Scientific journals)
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
Favorov, A.A.; Gelfand, M.S.; Gerasimova, A.V. et al.
2005In Bioinformatics, 21 (10), p. 2240-2245
Peer reviewed
 

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Abstract :
[en] Motivation: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency for highly divergent motifs as well as estimation of motif geometric parameters. Result: We present a modification of the Gibbs sampling motif extraction algorithm, SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo), which finds structured motifs of these types, as well as non-structured motifs, in a set of unaligned DNA sequences. It employs improved estimators of motif and spacer lengths. The probability that a sequence does not contain any motif is accounted for in a rigorous Bayesian manner. We have applied the algorithm to a set of upstream regions of genes from two Escherichia coli regulons involved in respiration. We have demonstrated that accounting for a symmetric motif structure allows the algorithm to identify weak motifs more accurately. In the examples studied, ArcA binding sites were demonstrated to have the structure of a direct spaced repeat, whereas NarP binding sites exhibited the palindromic structure. Availability: The WWW interface of the program, its FreeBSD (4.0) and Windows 32 console executables are available at http://bioinform.genetika.ru/SeSiMCMC
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Favorov, A.A.
Gelfand, M.S.
Gerasimova, A.V.
Ravcheev, Dmitry ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Mironov, A.A.
Makeev, V.J.
External co-authors :
yes
Language :
English
Title :
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
Publication date :
2005
Journal title :
Bioinformatics
ISSN :
1367-4803
eISSN :
1460-2059
Publisher :
Oxford University Press - Journals Department, Oxford, United Kingdom
Volume :
21
Issue :
10
Pages :
2240-2245
Peer reviewed :
Peer reviewed
Available on ORBilu :
since 12 May 2016

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