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dc.contributor.authorHossain, K.S.M. Tozammel
dc.date.accessioned2018-05-11T06:00:16Z
dc.date.available2018-05-11T06:00:16Z
dc.date.issued2016-11-16
dc.identifier.othervt_gsexam:8998en_US
dc.identifier.urihttp://hdl.handle.net/10919/83218
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_US
dc.format.mediumETDen_US
dc.publisherVirginia Techen_US
dc.rightsThis Item is protected by copyright and/or related rights. Some uses of this Item may be deemed fair and permitted by law even without permission from the rights holder(s), or the rights holder(s) may have licensed the work for use under certain conditions. For other uses you need to obtain permission from the rights holder(s).en_US
dc.subjectresidue couplingen_US
dc.subjectmultiple sequence alignmenten_US
dc.subjectgraphical modelsen_US
dc.subjectpattern set miningen_US
dc.titleModeling Evolutionary Constraints and Improving Multiple Sequence Alignments using Residue Couplingsen_US
dc.typeDissertationen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineComputer Science and Applicationsen_US
dc.contributor.committeechairRamakrishnan, Narendran
dc.contributor.committeememberBailey-Kellogg, Chrisen_US
dc.contributor.committeememberPrakash, Bodicherla Adityaen_US
dc.contributor.committeememberOnufriev, Alexeyen_US
dc.contributor.committeememberBaker, Nathan A.en_US


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