Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.

ABSTRACT: Classifying 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 infor

SUBMITTER: Santos MA 

PROVIDER: S-EPMC3001082 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature