{"id":{"repo_id":"washington","oai_identifier":"oai:digital.lib.washington.edu:1773/26004"},"canonical_url":"https://search.dev.ndltd.org/etd/washington/oai:digital.lib.washington.edu:1773/26004","repository":{"repo_id":"washington","name":"University of Washington","base_url":"https://digital.lib.washington.edu/server/oai/request"},"display":{"title":"Estimation and Comparison of HIV-Specific Substitution Matrices","abstract":"Amino acid substitution matrices are commonly used for sequence alignment, phylogenetic inference and sequence comparison. Empirical organism-specific substitution matrices constructed using only sequence data from a particular organism are thought to lead to more accurate analyses. In HIV research, the standard substitution matrices are the between- and within-host matrices estimated using HIV sequences introduced by Nickle et al. (2007). This thesis focuses on constructing more granular HIV-specific matrices (clade-specific matrices and gene-specific matrices) and comparing the matrices in a way that accounts for error in matrix estimation. Using standard errors of parameter estimates predicted from a two-part linear model, the analyses indicate statistically significant difference between HIV clade B and HIV clade C matrices as well as between HIV Env gene and HIV Gag gene matrices upon performing Bonferroni-corrected comparisons of 189 estimates of amino acid exchangeability parameters.","abstract_html":"Amino acid substitution matrices are commonly used for sequence alignment, phylogenetic inference and sequence comparison. Empirical organism-specific substitution matrices constructed using only sequence data from a particular organism are thought to lead to more accurate analyses. In HIV research, the standard substitution matrices are the between- and within-host matrices estimated using HIV sequences introduced by Nickle et al. (2007). This thesis focuses on constructing more granular HIV-specific matrices (clade-specific matrices and gene-specific matrices) and comparing the matrices in a way that accounts for error in matrix estimation. Using standard errors of parameter estimates predicted from a two-part linear model, the analyses indicate statistically significant difference between HIV clade B and HIV clade C matrices as well as between HIV Env gene and HIV Gag gene matrices upon performing Bonferroni-corrected comparisons of 189 estimates of amino acid exchangeability parameters.","abstract_has_math":false,"creators":["Kee, Jia Jin"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Edlefsen, Paul"],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-10-13","date_published":"2014-10-13","updated_at":"2026-07-24T05:58:01Z","subjects":[],"languages":["en_US"],"rights":["Copyright is held by the individual authors."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1773/26004","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Edlefsen, Paul"]},{"key":"dc:creator","label":"Author","values":["Kee, Jia Jin"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2014-10-13T16:50:39Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2014-10-13T16:50:39Z"]},{"key":"dc:date.issued","label":"Date","values":["2014-10-13"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright is held by the individual authors."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.other","label":"Dc Identifier Other","values":["Kee_washington_0250O_13682.pdf"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1773/26004"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis (Master's)--University of Washington, 2014"]},{"key":"dc:description.abstract","label":"Abstract","values":["Amino acid substitution matrices are commonly used for sequence alignment, phylogenetic inference and sequence comparison. Empirical organism-specific substitution matrices constructed using only sequence data from a particular organism are thought to lead to more accurate analyses. In HIV research, the standard substitution matrices are the between- and within-host matrices estimated using HIV sequences introduced by Nickle et al. (2007). This thesis focuses on constructing more granular HIV-specific matrices (clade-specific matrices and gene-specific matrices) and comparing the matrices in a way that accounts for error in matrix estimation. Using standard errors of parameter estimates predicted from a two-part linear model, the analyses indicate statistically significant difference between HIV clade B and HIV clade C matrices as well as between HIV Env gene and HIV Gag gene matrices upon performing Bonferroni-corrected comparisons of 189 estimates of amino acid exchangeability parameters."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Estimation and Comparison of HIV-Specific Substitution Matrices"]}]}],"canonical_facts":{"dc:contributor.advisor":["Edlefsen, Paul"],"dc:creator":["Kee, Jia Jin"],"dc:date.accessioned":["2014-10-13T16:50:39Z"],"dc:date.available":["2014-10-13T16:50:39Z"],"dc:date.issued":["2014-10-13"],"dc:description":["Thesis (Master's)--University of Washington, 2014"],"dc:description.abstract":["Amino acid substitution matrices are commonly used for sequence alignment, phylogenetic inference and sequence comparison. Empirical organism-specific substitution matrices constructed using only sequence data from a particular organism are thought to lead to more accurate analyses. In HIV research, the standard substitution matrices are the between- and within-host matrices estimated using HIV sequences introduced by Nickle et al. (2007). This thesis focuses on constructing more granular HIV-specific matrices (clade-specific matrices and gene-specific matrices) and comparing the matrices in a way that accounts for error in matrix estimation. Using standard errors of parameter estimates predicted from a two-part linear model, the analyses indicate statistically significant difference between HIV clade B and HIV clade C matrices as well as between HIV Env gene and HIV Gag gene matrices upon performing Bonferroni-corrected comparisons of 189 estimates of amino acid exchangeability parameters."],"dc:format.mimetype":["application/pdf"],"dc:identifier.other":["Kee_washington_0250O_13682.pdf"],"dc:identifier.uri":["http://hdl.handle.net/1773/26004"],"dc:language.iso":["en_US"],"dc:rights":["Copyright is held by the individual authors."],"dc:title":["Estimation and Comparison of HIV-Specific Substitution Matrices"],"dc:type":["Thesis"]},"updated_at":"2026-07-24T05:58:01Z"}