Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles

Matteo Comin, Morris Antonelli

2015

Abstract

Enhancers are stretches of DNA (100-1000 bp) that play a major role in development gene expression, evolution and disease. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Even if the binding of transcription factors is sequence-specific, the identification of functionally similar enhancers is very difficult and it cannot be carried out with traditional alignment-based techniques. In this paper we study the use of alignment-free measures for the classification of CRMs. However alignment-free measures are generally tied to a fixed resolution k. Here we propose an alignment-free statistic that is based on multiple resolution patterns derived from Entropic Profiles. Entropic Profile is a function of the genomic location that captures the importance of that region with respect to the whole genome. We evaluate several alignment-free statistics on simulated data and real mouse ChIP-seq sequences. The new statistic is highly successful in discriminating functionally related enhancers and, in almost all experiments, it outperforms fixed-resolution methods.

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Paper Citation


in Harvard Style

Comin M. and Antonelli M. (2015). Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 171-177. DOI: 10.5220/0005251001710177


in Bibtex Style

@conference{bioinformatics15,
author={Matteo Comin and Morris Antonelli},
title={Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={171-177},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005251001710177},
isbn={978-989-758-070-3},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Fast Alignment-free Comparison for Regulatory Sequences using Multiple Resolution Entropic Profiles
SN - 978-989-758-070-3
AU - Comin M.
AU - Antonelli M.
PY - 2015
SP - 171
EP - 177
DO - 10.5220/0005251001710177