UCHIME improves sensitivity and speed of chimera detection
Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causin...
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| Vydáno v: | Bioinformatics Ročník 27; číslo 16; s. 2194 - 2200 |
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| Hlavní autoři: | , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Oxford
Oxford University Press
15.08.2011
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| Témata: | |
| ISSN: | 1367-4803, 1367-4811, 1460-2059, 1367-4811 |
| On-line přístup: | Získat plný text |
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| Abstract | Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
Contact:
robert@drive5.com
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information:
Supplementary data are available at Bioinformatics online. |
|---|---|
| AbstractList | Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
Contact:
robert@drive5.com
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information:
Supplementary data are available at Bioinformatics online. Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online. Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.MOTIVATIONChimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.RESULTSWe describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.robert@drive5.comCONTACTrobert@drive5.comSource, binaries and data: http://drive5.com/uchime.AVAILABILITYSource, binaries and data: http://drive5.com/uchime.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online. Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. robert@drive5.com Source, binaries and data: http://drive5.com/uchime. Supplementary data are available at Bioinformatics online. |
| Author | Quince, Christopher Edgar, Robert C. Knight, Rob Haas, Brian J. Clemente, Jose C. |
| AuthorAffiliation | 1 Tiburon, CA, USA, 2 Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4 School of Engineering, University of Glasgow, Glasgow G12 8LT, UK |
| AuthorAffiliation_xml | – name: 1 Tiburon, CA, USA, 2 Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4 School of Engineering, University of Glasgow, Glasgow G12 8LT, UK |
| Author_xml | – sequence: 1 givenname: Robert C. surname: Edgar fullname: Edgar, Robert C. organization: 1Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK – sequence: 2 givenname: Brian J. surname: Haas fullname: Haas, Brian J. organization: 1Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK – sequence: 3 givenname: Jose C. surname: Clemente fullname: Clemente, Jose C. organization: 1Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK – sequence: 4 givenname: Christopher surname: Quince fullname: Quince, Christopher organization: 1Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK – sequence: 5 givenname: Rob surname: Knight fullname: Knight, Rob organization: 1Tiburon, CA, USA, 2Genome Sequencing and Analysis Program, The Broad Institute, Cambridge, MA 02142, 3Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and 4School of Engineering, University of Glasgow, Glasgow G12 8LT, UK |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24411747$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/21700674$$D View this record in MEDLINE/PubMed |
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| Snippet | Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or... Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal... |
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| SubjectTerms | Algorithms Biological and medical sciences Computational Biology Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Original Papers Polymerase Chain Reaction Sequence Analysis, DNA - methods Software |
| Title | UCHIME improves sensitivity and speed of chimera detection |
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