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

Hartmann, Martin, Howes, Charles G., Veldre, Vilmar, Schneider, Salome, Vaishampayan, Parag A., Yannarell, Anthony C., Quince, Christopher, Johansson, Per, Björkroth, K. Johanna, Abarenkov, Kessy, Hallam, Steven J., Mohn, William W. and Nilsson, R. Henrik (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. ISSN 0378-1097

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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.

Item Type: Article
Uncontrolled Keywords: 16s sequence,hidden markov models,hmmer,reverse complementary,software,ssu rrna gene,microbiology,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/2400/2404
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 12 Sep 2022 10:32
Last Modified: 23 Sep 2022 02:53
URI: https://ueaeprints.uea.ac.uk/id/eprint/88120
DOI: 10.1111/j.1574-6968.2011.02274.x

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