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Bioinformatics. 2006 Aug 1;22(15):1917-8. Epub 2006 Jun 9.

tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.

Author information

1
Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute Beutenbergstr. 11, 07745 Jena, Germany. szafrans@fli-leibniz.de

Abstract

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.

PMID:
16766553
DOI:
10.1093/bioinformatics/btl277
[Indexed for MEDLINE]

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