A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES

Erola Pairo, Santiago Marco, Alexandre Perera

2010

Abstract

Transcription Factor binding sites are short and degenerate sequences, located mostly at the promoter of the gene, where some proteins bind in order to regulate transcription. Locating these sequences is an important issue, and many experimental and computational methods have been developed. Algorithms to search binding sites are usually based on Position Specific Scoring Matrices (PSSM), where each position is treated independently. Mapping symbolical DNA to numerical sequences, a detector has been built with a Principal Component Analysis of the numerical sequences, taking into account covariances between positions. When a treatment of missing values is incorporated the Q-residuals detector, based on PCA, performs better than a PSSM algorithm. The performance on the detector depends on the estimation of missing values and the percentage of missing values considered in the model.

Paper Citation

in Harvard Style

Pairo E., Marco S. and Perera A. (2010). A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 102-107. DOI: 10.5220/0002697301020107

in Bibtex Style

@conference{bioinformatics10,
author={Erola Pairo and Santiago Marco and Alexandre Perera},
title={A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={102-107},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002697301020107},
isbn={978-989-674-019-1},
}

in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - A SUBSPACE METHOD FOR THE DETECTION OF TRANSCRIPTION FACTOR BINDING SITES
SN - 978-989-674-019-1
AU - Pairo E.
AU - Marco S.
AU - Perera A.
PY - 2010
SP - 102
EP - 107
DO - 10.5220/0002697301020107