Improving the consistency of domain annotation within the Conserved Domain Database

Database : the Journal of Biological Databases and Curation
Myra K DerbyshireAron Marchler-Bauer

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.

References

Oct 9, 2002·Genome Research·Lewis Y GeerStephen H Bryant
Apr 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Lachlan CoinRichard Durbin
Jun 25, 2004·Nucleic Acids Research·Aron Marchler-Bauer, Stephen H Bryant
Oct 23, 2008·Nucleic Acids Research·William KlimkeTatiana Tatusova
Nov 6, 2008·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Nov 27, 2010·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Dec 1, 2012·Nucleic Acids Research·Daniel H HaftErin Beck
Dec 1, 2012·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Oct 11, 2014·Nucleic Acids Research·Ivica LetunicPeer Bork
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium

❮ Previous
Next ❯

Citations

Apr 1, 2015·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Srenivas Varadarajan, Lina J Karam
Oct 3, 2015·The Journal of Laryngology and Otology·S S Bakshi
Sep 12, 2015·The Journal of General Virology·Bas B Oude MunninkLia van der Hoek
Jan 16, 2010·BMC Genomics·Haisheng NieMartien A M Groenen
Jul 12, 2016·PLoS Computational Biology·Cuncong ZhongShibu Yooseph
Nov 20, 2019·Journal of Bacteriology·Michael Y Galperin, Shan-Ho Chou

❮ Previous
Next ❯

Software Mentioned

RPS
Search
COG
CDD
Batch
SMART
CD
- Search
Pfam
BLAST

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Nucleic Acids Research
Aron Marchler-BauerStephen H Bryant
Nucleic Acids Research
Aron Marchler-BauerStephen H Bryant
Nucleic Acids Research
Aron Marchler-Bauer, Stephen H Bryant
© 2021 Meta ULC. All rights reserved