A LOSSLESS COMPRESSION ALGORITHM FOR DNA SEQUENCES

Taysir H. A. Soliman, Tarek F. Gharib, Alshaimaa Abo-Alian, Mohammed Alsharkawy

2008

Abstract

Homology search is the seed for both genomics and proteomics research. However, the increase of the amount of DNA sequences requires efficient computational algorithms for performing sequence comparison and analysis. This is due to the fact that standard compression algorithms are not able to compress DNA sequences because they do not consider special characteristics of DNA sequences (i.e. DNA sequences contain several approximate repeats and complimentary palindromes are frequent in DNA). Recently, new algorithms have been proposed to compress DNA sequences, often using detection of long approximate repeats. The current work proposes a Lossless Compression Algorithm (LCA), providing a new encoding method. LCA achieves a better compression ratio than that of existing DNA-oriented compression algorithms, when compared to GenCompress and DNACompress, using nine different datasets.

Paper Citation

in Harvard Style

H. A. Soliman T., F. Gharib T., Abo-Alian A. and Alsharkawy M. (2008). A LOSSLESS COMPRESSION ALGORITHM FOR DNA SEQUENCES . In Proceedings of the Tenth International Conference on Enterprise Information Systems - Volume 2: ICEIS, ISBN 978-989-8111-37-1, pages 435-441. DOI: 10.5220/0001683504350441

in Bibtex Style

@conference{iceis08,
author={Taysir H. A. Soliman and Tarek F. Gharib and Alshaimaa Abo-Alian and Mohammed Alsharkawy},
title={A LOSSLESS COMPRESSION ALGORITHM FOR DNA SEQUENCES},
booktitle={Proceedings of the Tenth International Conference on Enterprise Information Systems - Volume 2: ICEIS,},
year={2008},
pages={435-441},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0001683504350441},
isbn={978-989-8111-37-1},
}

in EndNote Style

TY - CONF
JO - Proceedings of the Tenth International Conference on Enterprise Information Systems - Volume 2: ICEIS,
TI - A LOSSLESS COMPRESSION ALGORITHM FOR DNA SEQUENCES
SN - 978-989-8111-37-1
AU - H. A. Soliman T.
AU - F. Gharib T.
AU - Abo-Alian A.
AU - Alsharkawy M.
PY - 2008
SP - 435
EP - 441
DO - 10.5220/0001683504350441