Improving the consistency of domain annotation within the Conserved Domain Database

Database (Oxford). 2015 Mar 12:2015:bav012. doi: 10.1093/database/bav012. Print 2015.


When annotating protein sequences with the footprints of evolutionarily conserved domains, conservative score or E-value thresholds need to be applied for RPS-BLAST hits, to avoid many false positives. We notice that manual inspection and classification of hits gathered at a higher threshold can add a significant amount of valuable domain annotation. We report an automated algorithm that 'rescues' valuable borderline-scoring domain hits that are well-supported by domain architecture (DA, the sequential order of conserved domains in a protein query), including tandem repeats of domain hits reported at a more conservative threshold. This algorithm is now available as a selectable option on the public conserved domain search (CD-Search) pages. We also report on the possibility to 'suppress' domain hits close to the threshold based on a lack of well-supported DA and to implement this conservatively as an option in live conserved domain searches and for pre-computed results. Improving domain annotation consistency will in turn reduce the fraction of NR sequences with incomplete DAs.

Publication types

  • Dataset
  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms*
  • Databases, Protein*
  • Molecular Sequence Annotation / methods*
  • Protein Structure, Tertiary
  • Sequence Analysis, Protein / methods*