V-REVCOMP: Automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets

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

Research output: Contribution to journalArticlepeer-review

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 - 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 406781 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 analyse 1171646 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 nontrivial proportion of the entries were otherwise anomalous, including reverse complementary chimeras, sequences associated with wrong taxa, nonribosomal genes, sequences of poor quality or otherwise erroneous sequences without a 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.

Original languageEnglish (US)
Pages (from-to)140-145
Number of pages6
JournalFEMS microbiology letters
Volume319
Issue number2
DOIs
StatePublished - Jun 2011

Keywords

  • 16S sequence
  • HMMER
  • Hidden Markov models
  • Reverse complementary
  • SSU rRNA gene
  • Software

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Genetics

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