Physico-chemical properties of DNA in phylogeny construction

Yasin Bakiş, O. Ǔur Sezerman, Hasan H. Otu

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

Abstract

Phylogenic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) to find the distances between the sequences which is not a parameter dependent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physicochemical properties of DNA. RCM gives as good results as the distance determination method and among the physicochemical properties, Keto/Amino grouping is found to give the most accurate tree which is topological closest to the desired phylogeny.

Original languageEnglish (US)
Title of host publication2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010
Pages27-30
Number of pages4
DOIs
StatePublished - Jul 16 2010
Event2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010 - Antalya, Turkey
Duration: Apr 20 2010Apr 22 2010

Publication series

Name2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010

Other

Other2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010
CountryTurkey
CityAntalya
Period4/20/104/22/10

Fingerprint

Phylogeny
Chemical properties
DNA
DNA sequences
Sequence Alignment
Candida

Keywords

  • Candida
  • DNA
  • Phylogenetics
  • Physico-chemical properties
  • Reduced alphabets
  • Relative complexity measure

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Bakiş, Y., Ǔur Sezerman, O., & Otu, H. H. (2010). Physico-chemical properties of DNA in phylogeny construction. In 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010 (pp. 27-30). [5478912] (2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010). https://doi.org/10.1109/HIBIT.2010.5478912

Physico-chemical properties of DNA in phylogeny construction. / Bakiş, Yasin; Ǔur Sezerman, O.; Otu, Hasan H.

2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010. 2010. p. 27-30 5478912 (2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010).

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

Bakiş, Y, Ǔur Sezerman, O & Otu, HH 2010, Physico-chemical properties of DNA in phylogeny construction. in 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010., 5478912, 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010, pp. 27-30, 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010, Antalya, Turkey, 4/20/10. https://doi.org/10.1109/HIBIT.2010.5478912
Bakiş Y, Ǔur Sezerman O, Otu HH. Physico-chemical properties of DNA in phylogeny construction. In 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010. 2010. p. 27-30. 5478912. (2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010). https://doi.org/10.1109/HIBIT.2010.5478912
Bakiş, Yasin ; Ǔur Sezerman, O. ; Otu, Hasan H. / Physico-chemical properties of DNA in phylogeny construction. 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010. 2010. pp. 27-30 (2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010).
@inproceedings{6999c300d643409ab6806958f329db37,
title = "Physico-chemical properties of DNA in phylogeny construction",
abstract = "Phylogenic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) to find the distances between the sequences which is not a parameter dependent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physicochemical properties of DNA. RCM gives as good results as the distance determination method and among the physicochemical properties, Keto/Amino grouping is found to give the most accurate tree which is topological closest to the desired phylogeny.",
keywords = "Candida, DNA, Phylogenetics, Physico-chemical properties, Reduced alphabets, Relative complexity measure",
author = "Yasin Bakiş and {Ǔur Sezerman}, O. and Otu, {Hasan H.}",
year = "2010",
month = "7",
day = "16",
doi = "10.1109/HIBIT.2010.5478912",
language = "English (US)",
isbn = "9781424459704",
series = "2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010",
pages = "27--30",
booktitle = "2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010",

}

TY - GEN

T1 - Physico-chemical properties of DNA in phylogeny construction

AU - Bakiş, Yasin

AU - Ǔur Sezerman, O.

AU - Otu, Hasan H.

PY - 2010/7/16

Y1 - 2010/7/16

N2 - Phylogenic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) to find the distances between the sequences which is not a parameter dependent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physicochemical properties of DNA. RCM gives as good results as the distance determination method and among the physicochemical properties, Keto/Amino grouping is found to give the most accurate tree which is topological closest to the desired phylogeny.

AB - Phylogenic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) to find the distances between the sequences which is not a parameter dependent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physicochemical properties of DNA. RCM gives as good results as the distance determination method and among the physicochemical properties, Keto/Amino grouping is found to give the most accurate tree which is topological closest to the desired phylogeny.

KW - Candida

KW - DNA

KW - Phylogenetics

KW - Physico-chemical properties

KW - Reduced alphabets

KW - Relative complexity measure

UR - http://www.scopus.com/inward/record.url?scp=77954497977&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77954497977&partnerID=8YFLogxK

U2 - 10.1109/HIBIT.2010.5478912

DO - 10.1109/HIBIT.2010.5478912

M3 - Conference contribution

AN - SCOPUS:77954497977

SN - 9781424459704

T3 - 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010

SP - 27

EP - 30

BT - 2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010

ER -