loading
Papers

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Matej Lexa 1 ; Marie Brázdová 2 ; Lucie Navrátilová 2 and Karel Nejedlý 3

Affiliations: 1 Masaryk University, Czech Republic ; 2 Czech Academy of Sciences v.v.i., Czech Republic ; 3 Institute of Biophysics and Academy of Sciences of the Czech Republic, Czech Republic

ISBN: 978-989-8425-90-4

Keyword(s): Cruciforms, Simulation, Model, Stability, DNA, Superhelicity.

Related Ontology Subjects/Areas/Topics: Agents ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Enterprise Information Systems ; Information Systems Analysis and Specification ; Methodologies and Technologies ; Operational Research ; Sequence Analysis ; Simulation

Abstract: Sequence-dependent secondary DNA structures, such as cruciform or triplex DNA, are implicated in regulation of gene transcription and other important biological processes at the molecular level. Sequences capable of forming these structures can readily be identified in entire genomes by appropriate searching techniques. However, not every DNA segment containing the proper sequence has equal probability of forming an alternative structure. Calculating the free energy of the potential structures provides an estimate of their stability in vivo, but there are other structural factors, both local and non-local, not taken into account by such simplistic approach. In is paper we present the procedure we currently use to identify potential cruciform structures in DNA sequences. The procedure relies on identification of palindromes (or inverted repeats) and their evaluation by a nucleic acid folding program (UNAFold). We further extended the procedure by adding a modelling step to filter the p redicted cruciforms. The model takes into account superhelical density of the analyzed segments of DNA and calculates the probability of cruciforms forming at several locations of the analyzed DNA, based on the sequences in the stem and loop areas of the structures and competition among them. (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 3.228.24.192

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:
Lexa, M.; Navrátilová, L.; Nejedlý, K. and Brázdová, M. (2012). PREDICTION OF SIGNIFICANT CRUCIFORM STRUCTURES FROM SEQUENCE IN TOPOLOGICALLY CONSTRAINED DNA - A Probabilistic Modelling Approach.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 124-130. DOI: 10.5220/0003705701240130

@conference{bioinformatics12,
author={Matej Lexa. and Lucie Navrátilová. and Karel Nejedlý. and Marie Brázdová.},
title={PREDICTION OF SIGNIFICANT CRUCIFORM STRUCTURES FROM SEQUENCE IN TOPOLOGICALLY CONSTRAINED DNA - A Probabilistic Modelling Approach},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={124-130},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003705701240130},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - PREDICTION OF SIGNIFICANT CRUCIFORM STRUCTURES FROM SEQUENCE IN TOPOLOGICALLY CONSTRAINED DNA - A Probabilistic Modelling Approach
SN - 978-989-8425-90-4
AU - Lexa, M.
AU - Navrátilová, L.
AU - Nejedlý, K.
AU - Brázdová, M.
PY - 2012
SP - 124
EP - 130
DO - 10.5220/0003705701240130

Login or register to post comments.

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