Genomic sequence analysis using gap sequences and pattern filtering

S. C. Su, C. H. Yeh, C. C. Jay Kuo

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

Abstract

A new pattern filtering technique is developed to analyze the genomic sequence in this research based on gap sequences, in which the distance of the same symbol is recorded consecutively as a sequence of integers. Sequence alignment and similarity testing can be performed on a family of gap sequences over selected patterns. The gap sequence offers a new way for sequence structural analysis. The match between the gap sequences is considered as a frame match while a true match requires both frame and stuffing match. Simulation results show that the extension of gap match indicates the corresponding segment extension in the original genomic sequence. Thus, we are able to generalize the conventional alignment and scoring methods in a more adaptive way.

Original languageEnglish
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages539-540
Number of pages2
ISBN (Electronic)0769520006, 9780769520001
DOIs
Publication statusPublished - 2003
Externally publishedYes
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: 2003 Aug 112003 Aug 14

Publication series

NameProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Conference

Conference2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/TerritoryUnited States
CityStanford
Period2003/08/112003/08/14

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

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