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

Improving the consistency of domain annotation within the Conserved Domain Database.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA.
2
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA bauer@ncbi.nlm.nih.gov.

Abstract

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.

PMID:
25767294
PMCID:
PMC4356950
DOI:
10.1093/database/bav012
[Indexed for MEDLINE]
Free PMC Article

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