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PubMed · 16766553

tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.

Karol Szafranski·Niels Jahn·Matthias Platzer
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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.

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AlgorithmsArtifactsBase SequenceChromosome MappingModels, GeneticModels, StatisticalMolecular Sequence DataNucleotidesSequence AlignmentSequence Analysis, DNASequence Homology, Nucleic AcidSoftwareStochastic ProcessesJournal ArticleResearch Support, Non-U.S. Gov't

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Karol Szafranski, Niels Jahn, Matthias Platzer. 2006-06-09. tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.. https://doi.org/10.1093/bioinformatics%2Fbtl277

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