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Bioinformatics Advance Access originally published online on June 9, 2006
Bioinformatics 2006 22(15):1917-1918; 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

tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression

Karol Szafranski *, Niels Jahn and Matthias Platzer

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

*To whom correspondence should be addressed.

Summary: The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kb 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.

Contact: szafrans@fli-leibniz.de

Received on March 14, 2006; revised on May 19, 2006; accepted on May 29, 2006

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