Finding LPRs in DNA sequences based on a new index - SUA

Di Wang; Guoren Wang; Qingquan Wu; Baichen Chen

doi:10.1109/BIBE.2005.31

Finding LPRs in DNA sequences based on a new index - SUA

Di Wang^*, Guoren Wang, Qingquan Wu, Baichen Chen

^*Corresponding author for this work

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

14 Citations (Scopus)

Abstract

This paper proposes a new concept of repetitions, the Largest Pattern Repetition (the LPR) and a concept of pattern unit. A lightweight index structure, namely, the Succeeding Unit Array (the SUA) is designed based on pattern unit. The SUA decreases the space consumption efficiently and solves the space bottleneck in the search of repetitions. On the SUA all the atomic patterns which constitute the LPRs can be detected and the LPRs can be identified by connecting the same patterns. The theoretical analysis and experimental results show that both space and time complexity of the algorithms is O(n).

Original language	English
Title of host publication	Proceedings - BIBE 2005
Subtitle of host publication	5th IEEE Symposium on Bioinformatics and Bioengineering
Pages	281-284
Number of pages	4
DOIs	https://doi.org/10.1109/BIBE.2005.31
Publication status	Published - 2005
Externally published	Yes
Event	BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering - Minneapolis, MN, United States Duration: 19 Oct 2005 → 21 Oct 2005

Publication series

Name	Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering
Volume	2005

Conference

Conference	BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering
Country/Territory	United States
City	Minneapolis, MN
Period	19/10/05 → 21/10/05

Access to Document

10.1109/BIBE.2005.31

Cite this

@inproceedings{c3c98fce2e774ee5a3e2743d33eacfdc,

title = "Finding LPRs in DNA sequences based on a new index - SUA",

abstract = "This paper proposes a new concept of repetitions, the Largest Pattern Repetition (the LPR) and a concept of pattern unit. A lightweight index structure, namely, the Succeeding Unit Array (the SUA) is designed based on pattern unit. The SUA decreases the space consumption efficiently and solves the space bottleneck in the search of repetitions. On the SUA all the atomic patterns which constitute the LPRs can be detected and the LPRs can be identified by connecting the same patterns. The theoretical analysis and experimental results show that both space and time complexity of the algorithms is O(n).",

author = "Di Wang and Guoren Wang and Qingquan Wu and Baichen Chen",

year = "2005",

doi = "10.1109/BIBE.2005.31",

language = "English",

isbn = "0769524761",

series = "Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering",

pages = "281--284",

booktitle = "Proceedings - BIBE 2005",

note = "BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering ; Conference date: 19-10-2005 Through 21-10-2005",

}

Wang, D, Wang, G, Wu, Q & Chen, B 2005, Finding LPRs in DNA sequences based on a new index - SUA. in Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering., 1544481, Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering, vol. 2005, pp. 281-284, BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering, Minneapolis, MN, United States, 19/10/05. https://doi.org/10.1109/BIBE.2005.31

Finding LPRs in DNA sequences based on a new index - SUA. / Wang, Di; Wang, Guoren; Wu, Qingquan et al.
Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering. 2005. p. 281-284 1544481 (Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering; Vol. 2005).

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

TY - GEN

T1 - Finding LPRs in DNA sequences based on a new index - SUA

AU - Wang, Di

AU - Wang, Guoren

AU - Wu, Qingquan

AU - Chen, Baichen

PY - 2005

Y1 - 2005

N2 - This paper proposes a new concept of repetitions, the Largest Pattern Repetition (the LPR) and a concept of pattern unit. A lightweight index structure, namely, the Succeeding Unit Array (the SUA) is designed based on pattern unit. The SUA decreases the space consumption efficiently and solves the space bottleneck in the search of repetitions. On the SUA all the atomic patterns which constitute the LPRs can be detected and the LPRs can be identified by connecting the same patterns. The theoretical analysis and experimental results show that both space and time complexity of the algorithms is O(n).

AB - This paper proposes a new concept of repetitions, the Largest Pattern Repetition (the LPR) and a concept of pattern unit. A lightweight index structure, namely, the Succeeding Unit Array (the SUA) is designed based on pattern unit. The SUA decreases the space consumption efficiently and solves the space bottleneck in the search of repetitions. On the SUA all the atomic patterns which constitute the LPRs can be detected and the LPRs can be identified by connecting the same patterns. The theoretical analysis and experimental results show that both space and time complexity of the algorithms is O(n).

UR - http://www.scopus.com/inward/record.url?scp=33746099853&partnerID=8YFLogxK

U2 - 10.1109/BIBE.2005.31

DO - 10.1109/BIBE.2005.31

M3 - Conference contribution

AN - SCOPUS:33746099853

SN - 0769524761

SN - 9780769524764

T3 - Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

SP - 281

EP - 284

BT - Proceedings - BIBE 2005

T2 - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Y2 - 19 October 2005 through 21 October 2005

ER -

Finding LPRs in DNA sequences based on a new index - SUA

Abstract

Publication series

Conference

Access to Document

Other files and links

Fingerprint

Cite this