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A probabilistic method for small RNA flowgram matching.

Author information

1
Computer Science and Engineering Department, University of California, Riverside, USA.

Abstract

The 454 pyrosequencing technology is gaining popularity as an alternative to traditional Sanger sequencing. While each method has comparative advantages over the other, certain properties of the 454 method make it particularly well suited for small RNA discovery. We here describe some of the details of the 454 sequencing technique, with an emphasis on the nature of the intrinsic sequencing errors and methods for mitigating their effect. We propose a probabilistic framework for small RNA discovery, based on matching 454 flowgrams against the target genome. We formulate flowgram matching as an analog of profile matching, and adapt several profile matching techniques for the task of matching flowgrams. As a result, we are able to recover some of the hits missed by existing methods and assign probability-based scores to them.

PMID:
18229677
PMCID:
PMC3137517
[Indexed for MEDLINE]
Free PMC Article

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