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V-RevComp: automated high-throughput detection of reverse complementary 16S ribosomal RNA gene sequences in large environmental and taxonomic datasets

Artikel i vetenskaplig tidskrift
Författare Martin Hartmann
Charles G. Howes
Vilmar Veldre
Salome Schneider
Parag A. Vaishampayan
Anthony C. Yannarell
Christopher Quince
Per Johansson
K. Johanna Björkroth
Kessy Abarenkov
Steven J. Hallam
William W. Mohn
R. Henrik Nilsson
Publicerad i FEMS Microbiology Letters
Volym 319
Nummer/häfte 2
Sidor 140-145
ISSN 0378-1097
Publiceringsår 2011
Publicerad vid Institutionen för växt- och miljövetenskaper
Sidor 140-145
Språk en
Länkar onlinelibrary.wiley.com/doi/10.1111...
Ämnesord software; SSU rRNA gene; 16S sequence; reverse complementary; Hidden Markov Model; HMMER
Ämneskategorier Programvaruteknik, Mikrobiologi, Bioinformatik och systembiologi, Terrestrisk ekologi, Marin ekologi, Biologisk systematik, Bakteriologi, Medicinsk mikrobiologi

Sammanfattning

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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