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The Ohio State University.

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Using structural information in modeling and multiple alignments for phylogenetics.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Using structural information in modeling and multiple alignments for phylogenetics./
Author:	Pan, Xueliang.
Description:	137 p.
Notes:	Adviser: Dennis K. Pearl.
Contained By:	Dissertation Abstracts International69-02B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoeng/servlet/advanced?query=3302205
ISBN:	9780549477679

Using structural information in modeling and multiple alignments for phylogenetics.
Pan, Xueliang.

Using structural information in modeling and multiple alignments for phylogenetics. - 137 p.

Adviser: Dennis K. Pearl.

Thesis (Ph.D.)--The Ohio State University, 2008.

Phylogenetic studies are increasingly based on structural biological data and on statistical formalization. That leads to the study of improved models and of extracting the maximum information from sequence data. In this research, I have proposed to incorporate the structural information in two areas that relate to phylogenetic inference: one is to use a spatial dependent substitution model for likelihood calculation in phylogenetic inference; the other is to use a gap distance measure for MSA evaluation. While the first application is to using an improved substitution models in phylogenetic inference, the second one focuses on the quality of the MSA produced by different alignment procedures.

ISBN: 9780549477679Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Using structural information in modeling and multiple alignments for phylogenetics.
LDR:03146nam 2200301 a 45 001 856648
005 20100709
008 100709s2008 ||||||||||||||||| ||eng d
020 $a 9780549477679
035 $a (UMI)AAI3302205
035 $a AAI3302205
040 $a UMI $c UMI
100 1 $a Pan, Xueliang. $3 1023482
245 1 0 $a Using structural information in modeling and multiple alignments for phylogenetics.
300 $a 137 p.
500 $a Adviser: Dennis K. Pearl.
500 $a Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0767.
502 $a Thesis (Ph.D.)--The Ohio State University, 2008.
520 $a Phylogenetic studies are increasingly based on structural biological data and on statistical formalization. That leads to the study of improved models and of extracting the maximum information from sequence data. In this research, I have proposed to incorporate the structural information in two areas that relate to phylogenetic inference: one is to use a spatial dependent substitution model for likelihood calculation in phylogenetic inference; the other is to use a gap distance measure for MSA evaluation. While the first application is to using an improved substitution models in phylogenetic inference, the second one focuses on the quality of the MSA produced by different alignment procedures.
520 $a The proposed spatial dependent model was based on our observation that the amino acids close to the functional core region tend to be conservative and these on the periphery are likely subject to mutation. So we proposed a substitution model with its rate for each amino acid dependent on its distance to the catalytic active center, or the functional core of the protein. The SD model has been implemented in the framework of Bayesian hierarchical model, the posterior distribution of the model parameters and the phylogenetic inference was estimated simultaneously using the MCMC Metropolis-Hastings algorithm. The SD model has been applied to 11 enzymes that are primarily to central metabolism that are found in species from all Kingdoms. The SD model is much better than the currently available substitution models in terms of fitness consistently for all examples.
520 $a Besides the modeling, we also use the structural information of the sequences for MSA evaluation. The fixed alignments used in phylogenetic studies are derived in advance of phylogenetic analysis. There are many different ways to construct these alignments. The gap measurement proposed here is based on the assumption of structural superposition, and it not only evaluates the alignment quality of those sequences with structural information, but also those sequences without structural information. This measurement can be used to select a better MSA for our phylogenetic analysis. Furthermore, it may lead to improvement of the sequence alignment.
590 $a School code: 0168.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biology, Biostatistics. $3 1018416
690 $a 0308
690 $a 0715
710 2 $a The Ohio State University. $3 718944
773 0 $t Dissertation Abstracts International $g 69-02B.
790 $a 0168
790 1 0 $a Pearl, Dennis K., $e advisor
791 $a Ph.D.
792 $a 2008
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoeng/servlet/advanced?query=3302205