FastGroup: A program to dereplicate libraries of 16S rDNA sequences

被引：38

作者：

Seguritan, Victor ^{[1
]}

Rohwer, Forest ^{[2
]}

机构：

[1] Univ San Diego, Dept Computat Sci San Diego State, San Diego, CA 92182 USA

[2] Univ San Diego, Dept Biol San Diego State, San Diego, CA 92182 USA

来源：

BMC BIOINFORMATICS | 2001年 / 2卷 / 1期

关键词：

Query Sequence; Neighbor Join; Ambiguous Basis; Percent Sequence Identity; Microbial Biogeography;

D O I：

10.1186/1471-2105-2-9

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Conclusions: The FastGroup program simplifies the dereplication of 16S rDNA sequence libraries and prepares the raw sequences for subsequent analyses.

引用

页数：8

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