FastGroup: a program to dereplicate libraries of 16S rDNA sequences - PubMed (original) (raw)

Comparative Study

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

V Seguritan et al. BMC Bioinformatics. 2001.

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 > or =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.

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Figures

Figure 1

Figure 1

Graphical User Interface (GUI) for FastGroup.

Figure 2

Figure 2

Schematic of bacterial 16S rDNA showing conserved and hypervariable regions. Detailed information about the primers and their superposition on the bacterial 16S rDNA can be found at

. Bact27F (5' AGA GTT TGA TCM TGG CTC AG 3') corresponds to positions 9–27 of the E. coli 16S rDNA and is similar to BSF8/20. Bact517 (5' ATT ACC GCG GCT GCT GG 3') corresponds to positions 517–534 of the E. coli 16S rDNA and is similar to BSF517/17. Bact1492R (5' TAC GGY TAC CTT GTT ACG ACT T 3') corresponds to positions 1492–1514 of the E. coli 16S rDNA. The approximate sites for hypervariable regions (V1-V3) are shown as shaded boxes.

Figure 3

Figure 3

Comparison of ClustalX and FastGroup analyses. An alignment of the 16S rDNA library was performed using ClustalX and a NJ tree was constructed. The "ClustalX Clades" were made by grouping end nodes separated by approximately 3% divergence (i.e., the combined branch lengths). Sequences grouped together by FastGroup, using default trimming criteria and 97% PSI, were identified on this tree and color-coded.

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References

    1. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology. 1998;180:4765–4774. - PMC - PubMed
    1. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990;345:60–63. doi: 10.1038/345060a0. - DOI - PubMed
    1. Gusfield D. Algorithms for Strings, Trees, and Sequences: Computer Science and Computational Biology New York: Cambridge University Press; 1997.
    1. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 1997;24:4876–4882. doi: 10.1093/nar/25.24.4876. - DOI - PMC - PubMed
    1. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994;22:4673–4680. - PMC - PubMed

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