Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences.

Applied and Environmental Microbiology
J F Robison-CoxD M Ward

Abstract

Detection of chimeric artifacts formed when PCR is used to retrieve naturally occurring small-subunit (SSU) rRNA sequences may rely on demonstrating that different sequence domains have different phylogenetic affiliations. We evaluated the CHECK_CHIMERA method of the Ribosomal Database Project and another method which we developed, both based on determining nearest neighbors of different sequence domains, for their ability to discern artificially generated SSU rRNA chimeras from authentic Ribosomal Database Project sequences. The reliability of both methods decreases when the parental sequences which contribute to chimera formation are more than 82 to 84% similar. Detection is also complicated by the occurrence of authentic SSU rRNA sequences that behave like chimeras. We developed a naive statistical test based on CHECK_CHIMERA output and used it to evaluate previously reported SSU rRNA chimeras. Application of this test also suggests that chimeras might be formed by retrieving SSU rRNAs as cDNA. The amount of uncertainty associated with nearest-neighbor analyses indicates that such tests alone are insufficient and that better methods are needed.

References

Jun 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E F DeLong
Jul 1, 1991·Journal of Bacteriology·T M SchmidtN R Pace
May 3, 1990·Nature·S J GiovannoniK G Field
Mar 1, 1994·Proceedings of the National Academy of Sciences of the United States of America·S M BarnsN R Pace
May 1, 1993·Applied and Environmental Microbiology·J A FuhrmanA A Davis
Feb 1, 1994·Applied and Environmental Microbiology·E D KopczynskiD M Ward
Jul 1, 1993·Nucleic Acids Research·N LarsenC R Woese
Jul 1, 1993·International Journal of Systematic Bacteriology·P H Sneath

❮ Previous
Next ❯

Citations

Nov 24, 1999·FEMS Microbiology Letters·M OhkumaT Kudo
May 7, 2003·Applied and Environmental Microbiology·Thorsten Stoeck, Slava Epstein
Sep 7, 2004·Bioinformatics·Juan M GonzalezCesareo Saiz-Jimenez
Dec 8, 2005·Applied and Environmental Microbiology·Kevin E AshelfordAndrew J Weightman
Nov 23, 2006·FEMS Microbiology Ecology·Alexandra ZuendorfThorsten Stoeck
Apr 11, 2007·Bioscience, Biotechnology, and Biochemistry·Naoya ShinzatoYoshio Watanabe
Feb 2, 2000·Applied and Environmental Microbiology·L RiemannF Azam
Jun 19, 2001·FEMS Microbiology Letters·G C BakerA R Suharto
Jun 4, 2005·Applied and Environmental Microbiology·Linda K DickKatharine G Field
Sep 6, 2003·Applied and Environmental Microbiology·Thorsten StoeckSlava S Epstein
Mar 27, 2003·International Journal of Systematic and Evolutionary Microbiology·Philip Hugenholtz, Thomas Huber
Nov 11, 2005·International Journal of Systematic and Evolutionary Microbiology·Sophie von der Heyden, Thomas Cavalier-Smith
Oct 2, 2008·Environmental Microbiology·Eva AlexanderThorsten Stoeck
Feb 24, 2001·Environmental Microbiology·T G LilburnJ A Breznak
Mar 2, 2002·Applied and Environmental Microbiology·Steven M Short, Curtis A Suttle
May 5, 2006·Applied and Environmental Microbiology·Anke BehnkeThorsten Stoeck
Dec 5, 1998·Microbiology and Molecular Biology Reviews : MMBR·D M WardM M Bateson
Apr 1, 1997·Applied and Environmental Microbiology·M G WiseL J Shimkets
Jan 1, 1997·Applied and Environmental Microbiology·K G FieldS J Giovannoni
Jun 1, 1996·Applied and Environmental Microbiology·J BornemanE W Triplett

❮ Previous
Next ❯

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.