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Sökning: WFRF:(Hallam K) > (2011)

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  • Hartmann, Martin, 1977, et al. (författare)
  • V-RevComp: automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets
  • 2011
  • Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097. ; 319:2, s. 140-145
  • Tidskriftsartikel (refereegranskat)abstract
    • Reverse complementary DNA sequences – sequences that are inadvertently given backwards with all purines and pyrimidines transposed – can affect sequence analysis detrimentally unless taken into account. We present an open-source, high-throughput software tool – V-RevComp (http://www.cmde.science.ubc.ca/mohn/software.html) – to detect and reorient reverse complementary entries of the small-subunit rRNA (16S) gene from sequencing datasets, particularly from environmental sources. The software supports sequence lengths ranging from full-length down to the short reads that are characteristic of next generation sequencing technologies. We evaluated the reliability of V-RevComp by screening all 406 781 16S sequences deposited in release 102 of the curated SILVA database and demonstrated that the tool has a detection accuracy of virtually 100%. We subsequently used V-RevComp to analyze 1 171 646 16S sequences deposited in the International Nucleotide Sequence Databases and found that about 1% of these user-submitted sequences were reverse complementary. In addition, a non-trivial proportion of entries were otherwise anomalous, including reverse complementary chimeras, sequences associated with wrong taxa, non-ribosomal genes, sequences of poor quality or otherwise erroneous sequences without reasonable match to any other entry in the database. Thus, V-RevComp is highly efficient in detecting and reorienting reverse complementary 16S sequences of almost any length and can be used to detect various sequence anomalies.
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