Protein subfamily assignment using the Conserved Domain Database.

ABSTRACT:

Background

Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD) that takes into account the organization of the domains into hierarchies of homologous domain models.

Findings

Our analysis of alignment scores from NCBI-curated domain assignments suggests that identifying the correct model among closely related models is more difficult than choosing between non-overlapping domain models. We find that simple heuristics based on sortin

SUBMITTER: Fong JH 

PROVIDER: S-EPMC2632666 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature