title: V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets.
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 analyse 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 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.
authors: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada. martinha@mail.ubc.ca
authors: Martin
authors: M
authors: Hartmann
authors: Charles G
authors: CG
authors: Howes
authors: Vilmar
authors: V
authors: Veldre
authors: Salome
authors: S
authors: Schneider
authors: Parag A
authors: PA
authors: Vaishampayan
authors: Anthony C
authors: AC
authors: Yannarell
authors: Christopher
authors: C
authors: Quince
authors: Per
authors: P
authors: Johansson
authors: K Johanna
authors: KJ
authors: Björkroth
authors: Kessy
authors: K
authors: Abarenkov
authors: Steven J
authors: SJ
authors: Hallam
authors: William W
authors: WW
authors: Mohn
authors: R Henrik
authors: RH
authors: Nilsson
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D030561:Databases, Nucleic Acid; D004783:Environmental Microbiology; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S