CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats.

Database : the Journal of Biological Databases and Curation
Alejandro RubioAntonio J Pérez-Pulido

Abstract

The genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing clustered regularly interspaced short palindromic repeats. We therefore encourage developers of prokaryotic computational gene finders and protein database curators to consider this source of error.

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 26, 2003·Nucleic Acids Research·Stéphanie BocsClaudine Médigue
Jan 24, 2007·BMC Bioinformatics·Robert C Edgar
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Jul 19, 2013·Database : the Journal of Biological Databases and Curation·Alinda Nagy, László Patthy
Mar 20, 2014·Bioinformatics·Torsten Seemann
Dec 5, 2014·PLoS Computational Biology·James F DentonMatthew W Hahn
Jul 24, 2015·Standards in Genomic Sciences·Supratim MukherjeeAmrita Pati
Oct 24, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Juan JimenezAntonio J Perez-Pulido
May 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Kazuharu Arakawa
Jun 28, 2016·Nucleic Acids Research·Tatiana TatusovaJames Ostell
Dec 3, 2016·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Jan 24, 2018·Journal of Bacteriology·Yoshizumi IshinoPatrick Forterre
May 4, 2018·F1000Research·Wolfram HöpsAlex Bateman
Oct 26, 2018·Nucleic Acids Research·Sara El-GebaliRobert D Finn
Oct 26, 2018·Nucleic Acids Research·Supratim MukherjeeTbk Reddy
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Apr 26, 2019·The CRISPR Journal·Alexandra B CrawleyRodolphe Barrangou
May 9, 2019·Genome Research·Florian P BreitwieserSteven L Salzberg
May 18, 2019·Genome Biology·Steven L Salzberg
Dec 21, 2019·Nature Reviews. Microbiology·Kira S MakarovaEugene V Koonin

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Datasets Mentioned

BETA
EMBL

Software Mentioned

BLAST
CRISPRCasFinder
RAST
Prokka
Prodigal
AMIGene
AnABlast
CRT
RASTtk
GeneMarkS

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.

© 2021 Meta ULC. All rights reserved