Algorithms for mapping short degenerate and weighted sequences to a reference genome

Pavlos Antoniou; Costas S. Iliopoulos; Laurent Mouchard; Solon P. Pissis

doi:10.1504/IJCBDD.2009.030768

Algorithms for mapping short degenerate and weighted sequences to a reference genome

Pavlos Antoniou, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis

Informatics

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design algorithms for Massive Exact and Approximate Pattern Matching of short degenerate and weighted sequences, derived from Deep sequencing technologies, to a reference genome.

Original language	Undefined/Unknown
Pages (from-to)	385 - 397
Number of pages	3
Journal	International Journal of Computational Biology and Drug Design
Volume	2
Issue number	4
DOIs	https://doi.org/10.1504/IJCBDD.2009.030768
Publication status	Published - 2010

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10.1504/IJCBDD.2009.030768

Cite this

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abstract = "Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design algorithms for Massive Exact and Approximate Pattern Matching of short degenerate and weighted sequences, derived from Deep sequencing technologies, to a reference genome.",

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AU - Iliopoulos, Costas S.

AU - Mouchard, Laurent

AU - Pissis, Solon P.

PY - 2010

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AB - Novel high-throughput (Deep) sequencing technologies have redefined the way genome sequencing is performed. They are able to produce millions of short sequences in a single experiment and with a much lower cost than previous methods. In this paper, we address the problem of efficiently mapping and classifying millions of short sequences to a reference genome, based on whether they occur exactly once in the genome or not, and by taking into consideration probability scores. In particular, we design algorithms for Massive Exact and Approximate Pattern Matching of short degenerate and weighted sequences, derived from Deep sequencing technologies, to a reference genome.

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DO - 10.1504/IJCBDD.2009.030768

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