P-Coffee: A New Divide-and-conquer Method for Multiple Sequence Alignment

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dc.contributor.advisor Dr. Subhashis Ghosal, Committee Member en_US
dc.contributor.advisor Dr. Dennis R. Bahler, Committee Chair en_US
dc.contributor.advisor Dr. Jon Doyle, Committee Member en_US
dc.contributor.author Choi, Kwangbom en_US
dc.date.accessioned 2010-04-02T17:57:45Z
dc.date.available 2010-04-02T17:57:45Z
dc.date.issued 2005-01-19 en_US
dc.identifier.other etd-01182005-060947 en_US
dc.identifier.uri http://www.lib.ncsu.edu/resolver/1840.16/692
dc.description.abstract We describe a new divide-and-conquer method, P-Coffee, for alignment of multiple sequences. P-Coffee first identifies candidate alignment columns using a position-specific substitution matrix (the T-Coffee extended library), tests those columns, and accepts only qualified ones. Accepted columns do not only constitute a final alignment solution, but also divide a given sequence set into partitions. The same procedure is recursively applied to each partition until all the alignment columns are collected. In P-Coffee, we minimized the source of bias by aligning all the sequences simultaneously without requiring any heuristic function to optmize, phylogenetic tree, nor gap cost scheme. In this research, we show the performance of our approach by comparing our results with that of T-Coffee using the 144 test sets provided in BAliBASE v1.0. P-Coffee outperformed T-Coffee in accuracy especially for more complicated test sets. en_US
dc.rights I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. en_US
dc.subject multiple sequence alignment en_US
dc.subject partition wall en_US
dc.subject wall identification en_US
dc.subject wall selection en_US
dc.title P-Coffee: A New Divide-and-conquer Method for Multiple Sequence Alignment en_US
dc.degree.name MS en_US
dc.degree.level thesis en_US
dc.degree.discipline Computer Science en_US

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