FastGroup A program to dereplicate libraries of 16S rDNA sequences.docVIP

BMC Bioinformatics BioMedCentral Methodology article BMC2001Bioinformatics, 2 :9 FastGroup: A program to dereplicate libraries of 16S rDNA sequences Victor Seguritan1 and Forest Rohwer*2 Address: 1Department of Computational Science San Diego State, University San Diego, California, 92182, USA and 2Department of Biology San Diego State, University San Diego, CA 92182, USA E-mail: Victor Seguritan - vsegurit@; Forest Rohwer* - forest@ *Corresponding author Published: 16 October 2001 Received: 14 May 2001 Accepted: 16 October 2001 BMC Bioinformatics 2001, 2:9 This article is available from: /1471-2105/2/9 ? 2001 Seguritan and Rohwer; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any non-commercial purpose, provided this notice is preserved along with the articles original URL. For commercial use, contact info@ Abstract Background: Ribosomal 16S DNA sequences are an essential tool for identifying and classifying microbes. High-throughput DNA sequencing now makes it economically possible to produce very large datasets of 16S rDNA sequences in short time periods, necessitating new computer tools for analyses. Here we describe FastGroup, a Java program designed to dereplicate libraries of 16S rDNA sequences. By dereplication we mean to: 1) compare all the sequences in a data set to each other, 2) group similar sequences together, and 3) output a representative sequence from each group. In this way, duplicate sequences are removed from a library. Results: FastGroup was tested using a library of single-pass, bacterial 16S rDNA sequences cloned from coral-associated bacteria. We found that the optimal strategy for dereplicating these sequences was to: 1) trim ambiguous bases from the 5 end of the sequences and all sequence 3 of the conserved Bact517 site, 2) match the sequences from the 3 end, and 3) group sequences =97% identical to each other.