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 - 2008
Event6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08 - Phoenix, AZ, United States
Duration: Jun 8 2008Jun 10 2008

Other

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

Fingerprint

Matching Pursuit
Sequence Alignment
DNA sequences
DNA Sequence
Decomposition
Decompose
Alignment
Nucleic Acid Repetitive Sequences
Misalignment
Protein Sequence
Cross-correlation
Decomposition Method
RNA
Grouping
Databases
Positioning
Signal Processing
Signal processing
DNA
Proteins

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] https://doi.org/10.1109/GENSIPS.2008.4555660

DNA sequence alignment using the matching pursuit decomposition. / Ravichandran, Lakshminarayan; Papandreou-Suppappola, Antonia; Spanias, Andreas; Lacroix, Zoé; Legendre, Christophe.

GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 2008. 4555660.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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, 6th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'08, Phoenix, AZ, United States, 6/8/08. https://doi.org/10.1109/GENSIPS.2008.4555660
Ravichandran L, Papandreou-Suppappola A, Spanias A, Lacroix Z, Legendre C. DNA sequence alignment using the matching pursuit decomposition. In GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 2008. 4555660 https://doi.org/10.1109/GENSIPS.2008.4555660
Ravichandran, Lakshminarayan ; Papandreou-Suppappola, Antonia ; Spanias, Andreas ; Lacroix, Zoé ; Legendre, Christophe. / DNA sequence alignment using the matching pursuit decomposition. GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 2008.
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