The phylogenetic tree of RNA Polymerase constructed using MOM method

Nora Muda, Abdul Rahman Othman, Nazalan Najimudin, Zeti Azura Mohamed Hussein

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

1 Citation (Scopus)

Abstract

Phylogenetic analysis is a study of evolutionary relationship between organisms or species, and the evolutionary is displayed as a phylogenetic tree. In this paper, the phylogenetic tree was constructed by using distance-based method; UPGMA and the proposed method, MOM estimator. The UPGMA calculates the average of possible pairwise distances to get a new distance in the clustering process. If outliers exist in the possible pairwise distances, new mean distances are calculated, and the result is not robust. To overcome this problem, we implement a checking process to detect the outliers using MAD n criteria on (based on median), and the new distances using the modified one-step M-estimator (MOM). In order to evaluate the branch of the tree constructed, the bootstrap method is used and the p-value (bootstrap value) for both methods is compared.

Original languageEnglish
Title of host publicationSoCPaR 2009 - Soft Computing and Pattern Recognition
Pages484-489
Number of pages6
DOIs
Publication statusPublished - 2009
EventInternational Conference on Soft Computing and Pattern Recognition, SoCPaR 2009 - Malacca
Duration: 4 Dec 20097 Dec 2009

Other

OtherInternational Conference on Soft Computing and Pattern Recognition, SoCPaR 2009
CityMalacca
Period4/12/097/12/09

Fingerprint

RNA

Keywords

  • Bootstrap
  • MAD
  • MOM estimator
  • UPGMA

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Vision and Pattern Recognition
  • Software

Cite this

Muda, N., Othman, A. R., Najimudin, N., & Mohamed Hussein, Z. A. (2009). The phylogenetic tree of RNA Polymerase constructed using MOM method. In SoCPaR 2009 - Soft Computing and Pattern Recognition (pp. 484-489). [5368642] https://doi.org/10.1109/SoCPaR.2009.99

The phylogenetic tree of RNA Polymerase constructed using MOM method. / Muda, Nora; Othman, Abdul Rahman; Najimudin, Nazalan; Mohamed Hussein, Zeti Azura.

SoCPaR 2009 - Soft Computing and Pattern Recognition. 2009. p. 484-489 5368642.

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

Muda, N, Othman, AR, Najimudin, N & Mohamed Hussein, ZA 2009, The phylogenetic tree of RNA Polymerase constructed using MOM method. in SoCPaR 2009 - Soft Computing and Pattern Recognition., 5368642, pp. 484-489, International Conference on Soft Computing and Pattern Recognition, SoCPaR 2009, Malacca, 4/12/09. https://doi.org/10.1109/SoCPaR.2009.99
Muda N, Othman AR, Najimudin N, Mohamed Hussein ZA. The phylogenetic tree of RNA Polymerase constructed using MOM method. In SoCPaR 2009 - Soft Computing and Pattern Recognition. 2009. p. 484-489. 5368642 https://doi.org/10.1109/SoCPaR.2009.99
Muda, Nora ; Othman, Abdul Rahman ; Najimudin, Nazalan ; Mohamed Hussein, Zeti Azura. / The phylogenetic tree of RNA Polymerase constructed using MOM method. SoCPaR 2009 - Soft Computing and Pattern Recognition. 2009. pp. 484-489
@inproceedings{15437af9778342dabd844f5f4651d689,
title = "The phylogenetic tree of RNA Polymerase constructed using MOM method",
abstract = "Phylogenetic analysis is a study of evolutionary relationship between organisms or species, and the evolutionary is displayed as a phylogenetic tree. In this paper, the phylogenetic tree was constructed by using distance-based method; UPGMA and the proposed method, MOM estimator. The UPGMA calculates the average of possible pairwise distances to get a new distance in the clustering process. If outliers exist in the possible pairwise distances, new mean distances are calculated, and the result is not robust. To overcome this problem, we implement a checking process to detect the outliers using MAD n criteria on (based on median), and the new distances using the modified one-step M-estimator (MOM). In order to evaluate the branch of the tree constructed, the bootstrap method is used and the p-value (bootstrap value) for both methods is compared.",
keywords = "Bootstrap, MAD, MOM estimator, UPGMA",
author = "Nora Muda and Othman, {Abdul Rahman} and Nazalan Najimudin and {Mohamed Hussein}, {Zeti Azura}",
year = "2009",
doi = "10.1109/SoCPaR.2009.99",
language = "English",
isbn = "9780769538792",
pages = "484--489",
booktitle = "SoCPaR 2009 - Soft Computing and Pattern Recognition",

}

TY - GEN

T1 - The phylogenetic tree of RNA Polymerase constructed using MOM method

AU - Muda, Nora

AU - Othman, Abdul Rahman

AU - Najimudin, Nazalan

AU - Mohamed Hussein, Zeti Azura

PY - 2009

Y1 - 2009

N2 - Phylogenetic analysis is a study of evolutionary relationship between organisms or species, and the evolutionary is displayed as a phylogenetic tree. In this paper, the phylogenetic tree was constructed by using distance-based method; UPGMA and the proposed method, MOM estimator. The UPGMA calculates the average of possible pairwise distances to get a new distance in the clustering process. If outliers exist in the possible pairwise distances, new mean distances are calculated, and the result is not robust. To overcome this problem, we implement a checking process to detect the outliers using MAD n criteria on (based on median), and the new distances using the modified one-step M-estimator (MOM). In order to evaluate the branch of the tree constructed, the bootstrap method is used and the p-value (bootstrap value) for both methods is compared.

AB - Phylogenetic analysis is a study of evolutionary relationship between organisms or species, and the evolutionary is displayed as a phylogenetic tree. In this paper, the phylogenetic tree was constructed by using distance-based method; UPGMA and the proposed method, MOM estimator. The UPGMA calculates the average of possible pairwise distances to get a new distance in the clustering process. If outliers exist in the possible pairwise distances, new mean distances are calculated, and the result is not robust. To overcome this problem, we implement a checking process to detect the outliers using MAD n criteria on (based on median), and the new distances using the modified one-step M-estimator (MOM). In order to evaluate the branch of the tree constructed, the bootstrap method is used and the p-value (bootstrap value) for both methods is compared.

KW - Bootstrap

KW - MAD

KW - MOM estimator

KW - UPGMA

UR - http://www.scopus.com/inward/record.url?scp=77649323924&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77649323924&partnerID=8YFLogxK

U2 - 10.1109/SoCPaR.2009.99

DO - 10.1109/SoCPaR.2009.99

M3 - Conference contribution

SN - 9780769538792

SP - 484

EP - 489

BT - SoCPaR 2009 - Soft Computing and Pattern Recognition

ER -