Genomic sequence analysis using gap sequences and pattern filtering

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

doi:10.1109/CSB.2003.1227401

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 proceeding › Conference contribution

1 Citation (Scopus)

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 language	English
Title of host publication	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	539-540
Number of pages	2
ISBN (Electronic)	0769520006, 9780769520001
DOIs	https://doi.org/10.1109/CSB.2003.1227401
Publication status	Published - 2003
Externally published	Yes
Event	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: 2003 Aug 11 → 2003 Aug 14

Publication series

Name	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Conference

Conference	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/Territory	United States
City	Stanford
Period	2003/08/11 → 2003/08/14

ASJC Scopus subject areas

Electrical and Electronic Engineering
Computer Science Applications

Access to Document

10.1109/CSB.2003.1227401

Cite this

Su, S. C., Yeh, C. H., & Jay Kuo, C. C. (2003). Genomic sequence analysis using gap sequences and pattern filtering. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 539-540). Article 1227401 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227401

Genomic sequence analysis using gap sequences and pattern filtering. / Su, S. C.; Yeh, C. H.; Jay Kuo, C. C.
Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 539-540 1227401 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Su, SC, Yeh, CH & Jay Kuo, CC 2003, Genomic sequence analysis using gap sequences and pattern filtering. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227401, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, Institute of Electrical and Electronics Engineers Inc., pp. 539-540, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 2003/08/11. https://doi.org/10.1109/CSB.2003.1227401

@inproceedings{09919193d48f48889c5cbaf51a4db737,

title = "Genomic sequence analysis using gap sequences and pattern filtering",

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.",

author = "Su, {S. C.} and Yeh, {C. H.} and {Jay Kuo}, {C. C.}",

note = "Publisher Copyright: {\textcopyright} 2003 IEEE.; 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 ; Conference date: 11-08-2003 Through 14-08-2003",

year = "2003",

doi = "10.1109/CSB.2003.1227401",

language = "English",

series = "Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "539--540",

booktitle = "Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003",

}

TY - GEN

T1 - Genomic sequence analysis using gap sequences and pattern filtering

AU - Su, S. C.

AU - Yeh, C. H.

AU - Jay Kuo, C. C.

PY - 2003

Y1 - 2003

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=36448961301&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=36448961301&partnerID=8YFLogxK

U2 - 10.1109/CSB.2003.1227401

DO - 10.1109/CSB.2003.1227401

M3 - Conference contribution

AN - SCOPUS:36448961301

T3 - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

SP - 539

EP - 540

BT - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003

Y2 - 11 August 2003 through 14 August 2003

ER -

Genomic sequence analysis using gap sequences and pattern filtering

Abstract

Publication series

Conference

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this