Sequence comparison using multi-order Markov chains

Xiang Fang, Guoqing Lu, Shunpu Zhang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phytogeny. Experiments with both simulated and real dataseis show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.

Original languageEnglish (US)
Title of host publication2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010
DOIs
StatePublished - Sep 6 2010
Event4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010 - Chengdu, China
Duration: Jun 18 2010Jun 20 2010

Publication series

Name2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010

Conference

Conference4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010
CountryChina
CityChengdu
Period6/18/106/20/10

Fingerprint

Markov Chains
DNA sequences
Markov processes
Phylogeny
Experiments

Keywords

  • Dna sequence
  • Markov chain
  • Multi-order transition matrix

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Fang, X., Lu, G., & Zhang, S. (2010). Sequence comparison using multi-order Markov chains. In 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010 [5515258] (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010). https://doi.org/10.1109/ICBBE.2010.5515258

Sequence comparison using multi-order Markov chains. / Fang, Xiang; Lu, Guoqing; Zhang, Shunpu.

2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010. 2010. 5515258 (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fang, X, Lu, G & Zhang, S 2010, Sequence comparison using multi-order Markov chains. in 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010., 5515258, 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010, 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010, Chengdu, China, 6/18/10. https://doi.org/10.1109/ICBBE.2010.5515258
Fang X, Lu G, Zhang S. Sequence comparison using multi-order Markov chains. In 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010. 2010. 5515258. (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010). https://doi.org/10.1109/ICBBE.2010.5515258
Fang, Xiang ; Lu, Guoqing ; Zhang, Shunpu. / Sequence comparison using multi-order Markov chains. 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010. 2010. (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010).
@inproceedings{36130c73b9b84bfeb6431be894756dae,
title = "Sequence comparison using multi-order Markov chains",
abstract = "DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phytogeny. Experiments with both simulated and real dataseis show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.",
keywords = "Dna sequence, Markov chain, Multi-order transition matrix",
author = "Xiang Fang and Guoqing Lu and Shunpu Zhang",
year = "2010",
month = "9",
day = "6",
doi = "10.1109/ICBBE.2010.5515258",
language = "English (US)",
isbn = "9781424447138",
series = "2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010",
booktitle = "2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010",

}

TY - GEN

T1 - Sequence comparison using multi-order Markov chains

AU - Fang, Xiang

AU - Lu, Guoqing

AU - Zhang, Shunpu

PY - 2010/9/6

Y1 - 2010/9/6

N2 - DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phytogeny. Experiments with both simulated and real dataseis show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.

AB - DNA sequences are often found to be composed of locally homogeneous segments that are functionally important. Most sequence comparison methods do not consider such a compositional property. We introduce a new method that takes this issue into consideration. With our method, the information of a DNA sequence is first transformed into a multi-order transition matrix (MTM); the resulting matrices are then used to compute pair-wise distances; and the consequent distances are used to construct molecular phytogeny. Experiments with both simulated and real dataseis show that the proposed method is able to reconstruct phylogenies consistent with those pre-defined or commonly accepted phylogenies.

KW - Dna sequence

KW - Markov chain

KW - Multi-order transition matrix

UR - http://www.scopus.com/inward/record.url?scp=77956161550&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77956161550&partnerID=8YFLogxK

U2 - 10.1109/ICBBE.2010.5515258

DO - 10.1109/ICBBE.2010.5515258

M3 - Conference contribution

SN - 9781424447138

T3 - 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010

BT - 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010

ER -