Please use this identifier to cite or link to this item: http://hdl.handle.net/2445/101507
Title: Sequence information gain based motif analysis
Author: Maynou, J.
Pairó, E.
Marco Colás, Santiago
Perera Lluna, Alexandre
Keywords: Genomes
Genètica humana
Genomes
Human genetics
Issue Date: 9-Nov-2015
Publisher: BioMed Central
Abstract: Background: The detection of regulatory regions in candidate sequences is essential for the understanding of the regulation of a particular gene and the mechanisms involved. This paper proposes a novel methodology based on information theoretic metrics for finding regulatory sequences in promoter regions. Results: This methodology (SIGMA) has been tested on genomic sequence data for Homo sapiens and Mus musculus. SIGMA has been compared with different publicly available alternatives for motif detection, such as MEME/MAST, Biostrings (Bioconductor package), MotifRegressor, and previous work such Qresiduals projections or information theoretic based detectors. Comparative results, in the form of Receiver Operating Characteristic curves, show how, in 70 % of the studied Transcription Factor Binding Sites, the SIGMA detector has a better performance and behaves more robustly than the methods compared, while having a similar computational time. The performance of SIGMA can be explained by its parametric simplicity in the modelling of the non-linear co-variability in the binding motif positions. Conclusions: Sequence Information Gain based Motif Analysis is a generalisation of a non-linear model of the cis-regulatory sequences detection based on Information Theory. This generalisation allows us to detect transcription factor binding sites with maximum performance disregarding the covariability observed in the positions of the training set of sequences. SIGMA is freely available to the public at http://​b2slab.​upc.​edu.
Note: Reproducció del document publicat a: http://dx.doi.org/10.1186/s12859-015-0811-x
It is part of: BMC Bioinformatics, 2015, vol. 16, num. 377
Related resource: http://dx.doi.org/10.1186/s12859-015-0811-x
URI: http://hdl.handle.net/2445/101507
ISSN: 1471-2105
Appears in Collections:Articles publicats en revistes (Electrònica)

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