Abstract

Sequence alignment is the positioning of primary biological sequences, such as DNA, RNA and protein sequences, to identify regions of similarity in large databases. Common signal processing techniques include cross-correlations in time or frequency. However, these techniques can result in many misalignments when capturing a grouping in local or repetitive portions of the sequence. We propose a time-frequency based alignment technique using the matching pursuit decomposition method and a mapping algorithm. The aim of this alignment technique is to identify local and global alignments more efficiently and with greater precision than existing methods. Its success is based on the fact that sequence elements are mapped to unique Gaussian basis atoms that uniformly sample the time-frequency plane.

Original languageEnglish (US)
Title of host publicationGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics
DOIs
StatePublished - Sep 17 2008
Event6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08 - Phoenix, AZ, United States
Duration: Jun 8 2008Jun 10 2008

Publication series

NameGENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics

Other

Other6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08
CountryUnited States
CityPhoenix, AZ
Period6/8/086/10/08

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ASJC Scopus subject areas

  • Genetics
  • Signal Processing
  • Electrical and Electronic Engineering
  • Statistics, Probability and Uncertainty

Cite this

Ravichandran, L., Papandreou-Suppappola, A., Spanias, A., Lacroix, Z., & Legendre, C. (2008). DNA sequence alignment using the matching pursuit decomposition. In GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics [4555660] (GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics). https://doi.org/10.1109/GENSIPS.2008.4555660