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. 2010 Aug 1;26(15):1901-2.
doi: 10.1093/bioinformatics/btq291. Epub 2010 Jun 18.

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

Brian D Ondov  1 , Charles Cochran, Mark Landers, Gavin D Meredith, Miroslav Dudas, Nicholas H Bergman
Affiliations

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

Brian D Ondov et al. Bioinformatics. .

Abstract

Summary: Bisulfite sequencing allows cytosine methylation, an important epigenetic marker, to be detected via nucleotide substitutions. Since the Applied Biosystems SOLiD System uses a unique di-base encoding that increases confidence in the detection of nucleotide substitutions, it is a potentially advantageous platform for this application. However, the di-base encoding also makes reads with many nucleotide substitutions difficult to align to a reference sequence with existing tools, preventing the platform's potential utility for bisulfite sequencing from being realized. Here, we present SOCS-B, a reference-based, un-gapped alignment algorithm for the SOLiD System that is tolerant of both bisulfite-induced nucleotide substitutions and a parametric number of sequencing errors, facilitating bisulfite sequencing on this platform. An implementation of the algorithm has been integrated with the previously reported SOCS alignment tool, and was used to align CpG methylation-enriched Arabidopsis thaliana bisulfite sequence data, exhibiting a 2-fold increase in sensitivity compared to existing methods for aligning SOLiD bisulfite data.

Availability: Executables, source code, and sample data are available at http://solidsoftwaretools.com/gf/project/socs/

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References

    1. Cokus SJ, et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215–219. - PMC - PubMed
    1. Frommer M, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA. 1992;89:1827–1831. - PMC - PubMed
    1. Karp RM, Rabin MO. Efficient randomized pattern-matching algorithms. IBM J. Res. Dev. 1987;31:249–260.
    1. Lister R, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133:523–536. - PMC - PubMed
    1. Ondov BD, et al. Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics. 2008;24:2776–2777. - PMC - PubMed

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