R C Edgar

• Uparse

  Open Access•R C Edgar•ARTICLE•Nature Methods•2013

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• Uchime improves sensitivity and speed of chimera detection

  Open Access•R C Edgar, Brian J Haas et al.•ARTICLE•Bioinformatics•2011

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  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 critic…

• Search and clustering orders of magnitude faster than BLAST

  Open Access•R C Edgar•ARTICLE•Bioinformatics•2010

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  Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST…

• Muscle

  Open Access•R C Edgar•ARTICLE•Nucleic Acids Research•2004

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  We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BA…

• Muscle

  Open Access•R C Edgar•ARTICLE•Nucleic Acids Research•2004

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  We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BA…

• Search and clustering orders of magnitude faster than BLAST

  Open Access•R C Edgar•ARTICLE•Bioinformatics•2010

  Añadir item

  Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST…

• Uchime improves sensitivity and speed of chimera detection

  Open Access•R C Edgar, Brian J Haas et al.•ARTICLE•Bioinformatics•2011

  Añadir item

  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 critic…

• Uparse

  Open Access•R C Edgar•ARTICLE•Nature Methods•2013

  Añadir item

Biology (4 obras) · Computer Science (4 obras) · Genomics and Phylogenetic Studies (4 obras) · Computational biology (2 obras) · Gene (2 obras) · Genetics (2 obras) · Machine learning (2 obras) · Microbial Community Ecology and Physiology (2 obras) · Polymerase chain reaction (2 obras) · 16S ribosomal RNA (1 obras)