loading
Papers

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Matteo Comin and Morris Antonelli

Affiliation: University of Padova, Italy

ISBN: 978-989-758-070-3

Keyword(s): Alignment-free, Sequence Comparison, Entropic Profiles.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Pattern Recognition, Clustering and Classification ; Sequence Analysis

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. (More)

PDF ImageFull Text

Download
CC BY-NC-ND 4.0

Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 34.204.168.57

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
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

@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},
}

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

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.