Back to Browse Journals » Advances and Applications in Bioinformatics and Chemistry » Volume 2

On calculating the probability of a set of orthologous sequences

Authors Junfeng Liu, Liang Chen, Hongyu Zhao, Dirk F Moore, Yong Lin, Weichung Joe Shih

Published Date February 2009 Volume 2009:2 Pages 37—48

DOI http://dx.doi.org/10.2147/AABC.S4616

Published 26 February 2009

Junfeng Liu1,2, Liang Chen3, Hongyu Zhao4, Dirk F Moore1,2, Yong Lin1,2, Weichung Joe Shih1,2

1Biometrics Division, The Cancer, Institute of New Jersey, New Brunswick, NJ, USA; 2Department of Biostatistics, School of Public Health, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA; 3Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 4Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA

Abstract: Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, this article investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA sequences which evolve from a common progenitor. We propose Monte Carlo integration algorithms to sample the unknown ancestral and/or root sequences a posteriori conditional on a reference sequence and apply pairwise Needleman–Wunsch alignment between the sampled and nonreference species sequences to estimate the probability. We test our algorithms on both simulated and real sequences and compare calculated probabilities from Monte Carlo integration to those induced by single multiple alignment.

Keywords: evolution, Jukes–Cantor model, Monte Carlo integration, Needleman–Wunsch alignment, orthologous

Download Article [PDF] 

Creative Commons License This work is published by Dove Medical Press Limited, and licensed under Creative Commons Attribution - Non Commercial (unported, v3.0) License. The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. Permissions beyond the scope of the License are administered by Dove Medical Press Limited. Information on how to request permission may be found at: http://www.dovepress.com/permissions.php

Readers of this article also read:

Proposed criteria for schizophrenia remission

AlAqeel B

Neuropsychiatric Disease and Treatment 2014, 10:619-623

Published Date: 16 April 2014

Inhibition of A/Human/Hubei/3/2005 (H3N2) influenza virus infection by silver nanoparticles in vitro and in vivo

Xiang DX, Zheng Y, Duan W, Li XJ, Yin JJ, Shigdar S, O'Connor ML, Marappan M, Zhao XJ, Miao YQ, Xiang B, Zheng CL

International Journal of Nanomedicine 2013, 8:4103-4114

Published Date: 30 October 2013

Making the certainty based marking pilot study a reality

Stone BA, Lemon TI

Advances in Medical Education and Practice 2013, 4:101-102

Published Date: 7 May 2013

Corrigendum

Brief G, Lammich T, Nagel E, Pfennigsdorf S, Spraul CW, Ho S

Clinical Ophthalmology 2012, 6:1271-1272

Published Date: 6 August 2012

Blood–brain barrier: a real obstacle for therapeutics

Shiekh FA

International Journal of Nanomedicine 2012, 7:4065-4067

Published Date: 27 July 2012

Corrigendum

De Caterina AR, Harper AR, Cuculi F

Vascular Health and Risk Management 2012, 8:443-445

Published Date: 19 July 2012

Corrigendum

Chen ZQ, Liu Y, Zhao JH, Wang L, Feng NP

International Journal of Nanomedicine 2012, 7:1709-1710

Published Date: 30 March 2012

Corrigendum: Softec HD hydrophilic acrylic intraocular lens: biocompatibility and precision

Espandar L, Sikder S, Moshirfar M

Clinical Ophthalmology 2011, 5:159-160

Published Date: 6 February 2011