Modeling Evolutionary Constraints and Improving Multiple Sequence Alignments using Residue Couplings

dc.contributor.authorHossain, K.S.M. Tozammelen
dc.contributor.committeechairRamakrishnan, Narenen
dc.contributor.committeememberBailey-Kellogg, Chrisen
dc.contributor.committeememberPrakash, B. Adityaen
dc.contributor.committeememberOnufriev, Alexey V.en
dc.contributor.committeememberBaker, Nathan A.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2018-05-11T06:00:16Zen
dc.date.available2018-05-11T06:00:16Zen
dc.date.issued2016-11-16en
dc.description.abstractResidue coupling in protein families has received much attention as an important indicator toward predicting protein structures and revealing functional insight into proteins. Existing coupling methods identify largely pairwise couplings and express couplings over amino acid combinations, which do not yield a mechanistic explanation. Most of these methods primarily use a multiple protein sequence alignment---most likely a resultant alignment---which better exposes couplings and is obtained through manual tweaking of an alignment constructed by a classical alignment algorithm. Classical alignment algorithms primarily focus on capturing conservations and may not fully unveil couplings in the alignment. In this dissertation, we propose methods for capturing both pairwise and higher-order couplings in protein families. Our methods provide mechanistic explanations for couplings using physicochemical properties of amino acids and discernibility between orders. We also investigate a method for mining frequent episodes---called coupled patterns---in an alignment produced by a classical algorithm for proteins and for exploiting the coupled patterns for improving the alignment quality in terms of exposition of couplings. We demonstrate the effectiveness of our proposed methods on a large collection of sequence datasets for protein families.en
dc.description.degreePh. D.en
dc.format.mediumETDen
dc.identifier.othervt_gsexam:8998en
dc.identifier.urihttp://hdl.handle.net/10919/83218en
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectresidue couplingen
dc.subjectmultiple sequence alignmenten
dc.subjectgraphical modelsen
dc.subjectpattern set miningen
dc.titleModeling Evolutionary Constraints and Improving Multiple Sequence Alignments using Residue Couplingsen
dc.typeDissertationen
thesis.degree.disciplineComputer Science and Applicationsen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.namePh. D.en

Files

Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Hossain_K_D_2016.pdf
Size:
1.44 MB
Format:
Adobe Portable Document Format