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dc.contributor.authorSantos, Miguel A.
dc.contributor.authorTurinsky, Andrei L.
dc.contributor.authorOng, Serene
dc.contributor.authorTsai, Jennifer
dc.contributor.authorBerger, Michael F.
dc.contributor.authorBadis, Gwenael
dc.contributor.authorTalukder, Shaheynoor
dc.contributor.authorGehrke, Andrew R.
dc.contributor.authorHughes, Timothy R.
dc.contributor.authorWodak, Shoshana J.
dc.contributor.authorBulyk, Martha Leonia
dc.date.accessioned2011-03-19T21:01:05Z
dc.date.issued2010
dc.identifier.citationSantos, Miguel A., Andrei L. Turinsky, Serene Ong, Jennifer Tsai, Michael F. Berger, Gwenael Badis, Shaheynoor Talukder, et al. 2010. Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. Nucleic Acids Research 38, no. 22: 7927-7942.en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4745743
dc.description.abstractClassifying proteins into subgroups with similar molecular function on the basis of sequence is an important step in deriving reliable functional annotations computationally. So far, however, available classification procedures have been evaluated against protein subgroups that are defined by experts using mainly qualitative descriptions of molecular function. Recently, in vitro DNA-binding preferences to all possible 8-nt DNA sequences have been measured for 178 mouse homeodomains using protein-binding microarrays, offering the unprecedented opportunity of evaluating the classification methods against quantitative measures of molecular function. To this end, we automatically derive homeodomain subtypes from the DNA-binding data and independently group the same domains using sequence information alone. We test five sequence-based methods, which use different sequence-similarity measures and algorithms to group sequences. Results show that methods that optimize the classification robustness reflect well the detailed functional specificity revealed by the experimental data. In some of these classifications, 73–83% of the subfamilies exactly correspond to, or are completely contained in, the function-based subtypes. Our findings demonstrate that certain sequence-based classifications are capable of yielding very specific molecular function annotations. The availability of quantitative descriptions of molecular function, such as DNA-binding data, will be a key factor in exploiting this potential in the future.en_US
dc.language.isoen_USen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofdoi://10.1093/nar/gkq714en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001082/pdf/en_US
dash.licenseLAA
dc.titleObjective Sequence-Based Subfamily Classifications of Mouse Homeodomains Reflect Their In Vitro DNA-Binding Preferencesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalNucleic Acids Researchen_US
dash.depositing.authorBulyk, Martha Leonia
dc.date.available2011-03-19T21:01:05Z
dash.affiliation.otherHMS^Pathologyen_US
dash.affiliation.otherHMS^Medicine-Brigham and Women's Hospitalen_US
dc.identifier.doi10.1093/nar/gkq714*
dash.authorsorderedfalse
dash.contributor.affiliatedBulyk, Martha


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