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

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, fac

SUBMITTER: Ondov BD 

PROVIDER: S-EPMC2905549 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature