tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.
CONCLUSIONS
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.


BACKGROUND
tuple_plot is available at http://genome.fli-leibniz.de/software.html and may be used under GNU public license.
Szafranski
Karol
K
Genome Analysis, Leibniz Institute for Age Research, Fritz Lipmann Institute Beutenbergstr. 11, 07745 Jena, Germany. szafrans@fli-leibniz.de
Jahn
Niels
N
Platzer
Matthias
M
D000465:Algorithms; D016477:Artifacts; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013269:Stochastic Processes
D009711:Nucleotides