title: Improving the consistency of domain annotation within the Conserved Domain Database.
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.
authors.affiliation: 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.
authors.forename: Myra K
authors.initials: MK
authors.lastname: Derbyshire
authors.affiliation: 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.
authors.forename: Noreen R
authors.initials: NR
authors.lastname: Gonzales
authors.affiliation: 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.
authors.forename: Shennan
authors.initials: S
authors.lastname: Lu
authors.affiliation: 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.
authors.forename: Jane
authors.initials: J
authors.lastname: He
authors.affiliation: 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.
authors.forename: Gabriele H
authors.initials: GH
authors.lastname: Marchler
authors.affiliation: 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.
authors.forename: Zhouxi
authors.initials: Z
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D058977:Molecular Sequence Annotation / Q000379:methods*; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein / Q000379:methods*