Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Troels T. Marstrand; Jes Frellsen; Ida Moltke; Martin Thiim; Eivind Valen; Dorota Retelska; Anders Krogh

doi:10.1371/journal.pone.0001623

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Open Access

Peer-reviewed

Research Article

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Troels T. Marstrand ,

*E-mail: dolle@binf.ku.dk

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯
Jes Frellsen,

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯
Ida Moltke,

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯
Martin Thiim,

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯
Eivind Valen,

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯
Dorota Retelska,

Affiliation Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research (ISREC), Epalinges, Switzerland
⨯
Anders Krogh

Affiliation Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
⨯

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Troels T. Marstrand,
Jes Frellsen,
Ida Moltke,
Martin Thiim,
Eivind Valen,
Dorota Retelska,
Anders Krogh

Published: February 20, 2008
https://doi.org/10.1371/journal.pone.0001623

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Possible misunderstanding

Posted by tmarstrand on 15 Apr 2008 at 10:56 GMT

As M. Beckstette has kindly pointed out the following sentence can by misunderstood:

"We have implemented a C library using a data structure called enhanced suffix arrays (ESA). Using a modified version of the ESAsearch algorithm, introduced by Beckstette et al. [17], we are able to solve the scoring problem with a speedup of as much as a factor 1000 compared to a naïve implementation (see supplementary material, text S1)."

We do not claim that it is our modifications that gives this speed-up. Rather it is achieved by the use of enhanced suffix arrays. We apologize for any misunderstandings.

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Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

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Possible misunderstanding

Posted by tmarstrand on 15 Apr 2008 at 10:56 GMT