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

Hartmann, M. et al. (2011) V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets. FEMS Microbiology Letters, 319(2), pp. 140-145. (doi: 10.1111/j.1574-6968.2011.02274.x)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Quince, Dr Christopher
• Authors: Hartmann, M., Howes, C.G., Veldre, V., Schneider, S., Vaishampayan, P.A., Yannarell, A.C., Quince, C., Johansson, P., Björkroth, K.J., Abarenkov, K., Hallam, S.J., Mohn, W.W., and Nilsson, R.H.
• College/School: College of Science and Engineering > School of Engineering > Infrastructure and Environment
• Journal Name: FEMS Microbiology Letters
• ISSN: 0378-1097
• Published Online: 27 April 2011