Show simple item record

dc.contributor.authorWang, Xuting
dc.date.accessioned2014-03-05T16:03:08Z
dc.date.available2014-03-05T16:03:08Z
dc.date.issued2002-05
dc.identifier.otherwang_xuting_200205_ms
dc.identifier.urihttp://purl.galileo.usg.edu/uga_etd/wang_xuting_200205_ms
dc.identifier.urihttp://hdl.handle.net/10724/29451
dc.description.abstractThe construction of multiple sequence alignments (MSAs) is a fundamental problem in computational biology, but computing an optimal MSA is NP-hard. It is therefore necessary to develop heuristics to come as close to the optimum as possible but operate within reasonable time and space bounds. In this thesis, an approach pioneered by Korostensky and Gonnet is developed and tested extensively. The idea is to apply a Traveling Salesman Problem (TSP) algorithm to find an optimal circular order to build an MSA progressively. The sum-of-pairs (SP) score is used for computing pairwise alignments and evaluating the quality of an MSA. Using the reference alignments from the benchmark alignment database BALISBASE, the performance of my program, tspMSA, was evaluated extensively with more than 60 reference data sets. Except for one test case, the SP scores obtained from the TSP algorithm are significant better than the scores obtained from two popular progressive alignment programs, PILEUP and CLUSTALW. The SP scores of MSAs built from different starting points and different directions of an optimal circular order are studied.
dc.languageMultiple sequence alignment using traveling salesman problem algorithms
dc.publisheruga
dc.rightspublic
dc.subjectmultiple sequence alignment
dc.subjectMSA
dc.subjecttraveling salesman problem
dc.subjectTSP
dc.subjectalgorithms
dc.subjectbranch-and-bound
dc.subjectglobal alignments
dc.subjectphylogenic tree
dc.subjectprogressive alignment
dc.titleMultiple sequence alignment using traveling salesman problem algorithms
dc.typeThesis
dc.description.degreeMS
dc.description.departmentComputer Science
dc.description.majorComputer Science
dc.description.advisorRobert W. Robinson
dc.description.committeeRobert W. Robinson
dc.description.committeeThiab R. Taha
dc.description.committeeE. Rodney Canfield


Files in this item

FilesSizeFormatView

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record