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Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays.

Abstract：

:Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally determining a polynucleotide sequence from its oligonucleotide content. We present here new methods that use such arrays for re-sequencing. Our methods are applied to data obtained by the polymerase signaling assay, which arrays single-based primer extension reactions for either universal or partial arrays of pentanucleotides. The computational analysis uses the spectrum alignment algorithm, which is refined and enhanced here in order to overcome noise incurred by the use of such short primers. We present accurate re-sequencing results for both synthetic and amplified DNA molecules.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Pe'er I,Arbili N,Liu Y,Enck C,Gelfand CA,Shamir R

doi

10.1093/nar/gkg757

keywords:

subject

Has Abstract

pub_date

2003-10-01 00:00:00

pages

5667-75

issue

19

eissn

0305-1048

issn

1362-4962

journal_volume

31

pub_type

杂志文章

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