Abstract

We investigate the use of time-frequency (TF) methods to query biological sequences in search of regions of similarity or critical relationships among the sequences. Existing querying approaches are insensitive to repeats, especially in low-complexity regions, and do not provide much support for efficiently querying sub-sequences with inserts and deletes (or gaps). Our approach uses highly-localized basis functions and multiple transformations in the TF plane to map characters in a sequence as well as different properties of a sub-sequence, such as its position in the sequence or number of gaps between sub-sequences. We analyze gapped query-based alignment methods using transformations in the TF plane while demonstrating the method's possible operation in real-time without pre-processing. The algorithm's performance is compared to the widely-accepted BLAST alignment approach, and a significance improvement is observed for queries with repetitive segments.

Original languageEnglish (US)
Title of host publication2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Proceedings
Pages4174-4177
Number of pages4
DOIs
StatePublished - Nov 8 2010
Event2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010 - Dallas, TX, United States
Duration: Mar 14 2010Mar 19 2010

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)1520-6149

Other

Other2010 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2010
CountryUnited States
CityDallas, TX
Period3/14/103/19/10

Keywords

  • Biological sequence querying
  • Gapped local alignment
  • Metaplectic transformations
  • Time-frequency methods

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

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