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Bioinformatics Advance Access published online on June 9, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl277
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 14, 2006
Revised May 19, 2006
Accepted May 29, 2006

Applications note

tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression

Karol Szafranski 1 *, Niels Jahn 1, and Matthias Platzer 1

1 Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany

* To whom correspondence should be addressed.
Karol Szafranski, E-mail: szafrans{at}fli-leibniz.de


  Abstract

Summary: The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kbp or longer, by applying the well-known dotplot principle. A dictionary of sequence words built from the input sequences serves to construct a task-specific expectancy model that is used to attribute significance values to pairwise word hits. The dictionary-based approach allows fast computation, the computation time scaling to O(N log N), depending on the size of the input sequences. The proposed scoring scheme appreciably increases the signal-to-noise ratio and may help to improve other word-based sequence comparison approaches.

Availability: tuple_plot is available at http://genome.fli-leibniz.de/software.html and may be used under GNU public license.

Associate Editor: Martin Bishop
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