Restricting SBH ambiguity via restriction enzymes

Steven Skiena; Sagi Snir

doi:10.1007/3-540-45784-4_30

Restricting SBH ambiguity via restriction enzymes

Steven Skiena, Sagi Snir

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

Abstract

The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

Original language	English
Title of host publication	Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings
Editors	Roderic Guigo, Dan Gusfield
Publisher	Springer Verlag
Pages	404-417
Number of pages	14
ISBN (Print)	3540442111, 9783540442110
DOIs	https://doi.org/10.1007/3-540-45784-4_30
State	Published - 2002
Externally published	Yes
Event	2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy Duration: 17 Sep 2002 → 21 Sep 2002

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	2452
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	2nd International Workshop on Algorithms in Bioinformatics, WABI 2002
Country/Territory	Italy
City	Rome
Period	17/09/02 → 21/09/02

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science (all)

Access to Document

10.1007/3-540-45784-4_30

Cite this

Skiena, S., & Snir, S. (2002). Restricting SBH ambiguity via restriction enzymes. In R. Guigo, & D. Gusfield (Eds.), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings (pp. 404-417). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452). Springer Verlag. https://doi.org/10.1007/3-540-45784-4_30

Skiena, Steven ; Snir, Sagi. / Restricting SBH ambiguity via restriction enzymes. Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. editor / Roderic Guigo ; Dan Gusfield. Springer Verlag, 2002. pp. 404-417 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{088c3975de7049949c4ecc60dffcbafe,

title = "Restricting SBH ambiguity via restriction enzymes",

abstract = "The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string{\textquoteright}s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.",

author = "Steven Skiena and Sagi Snir",

note = "Publisher Copyright: {\textcopyright} Springer-Verlag Berlin Heidelberg 2002.; 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 ; Conference date: 17-09-2002 Through 21-09-2002",

year = "2002",

doi = "10.1007/3-540-45784-4_30",

language = "English",

isbn = "3540442111",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "404--417",

editor = "Roderic Guigo and Dan Gusfield",

booktitle = "Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings",

address = "Germany",

}

Skiena, S & Snir, S 2002, Restricting SBH ambiguity via restriction enzymes. in R Guigo & D Gusfield (eds), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2452, Springer Verlag, pp. 404-417, 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002, Rome, Italy, 17/09/02. https://doi.org/10.1007/3-540-45784-4_30

Restricting SBH ambiguity via restriction enzymes. / Skiena, Steven; Snir, Sagi.
Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. ed. / Roderic Guigo; Dan Gusfield. Springer Verlag, 2002. p. 404-417 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452).

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

TY - GEN

T1 - Restricting SBH ambiguity via restriction enzymes

AU - Skiena, Steven

AU - Snir, Sagi

N1 - Publisher Copyright: © Springer-Verlag Berlin Heidelberg 2002.

PY - 2002

Y1 - 2002

N2 - The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

AB - The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

UR - http://www.scopus.com/inward/record.url?scp=23044532111&partnerID=8YFLogxK

U2 - 10.1007/3-540-45784-4_30

DO - 10.1007/3-540-45784-4_30

M3 - Conference contribution

AN - SCOPUS:23044532111

SN - 3540442111

SN - 9783540442110

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 404

EP - 417

BT - Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings

A2 - Guigo, Roderic

A2 - Gusfield, Dan

PB - Springer Verlag

T2 - 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002

Y2 - 17 September 2002 through 21 September 2002

ER -

Skiena S, Snir S. Restricting SBH ambiguity via restriction enzymes. In Guigo R, Gusfield D, editors, Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Springer Verlag. 2002. p. 404-417. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/3-540-45784-4_30

Restricting SBH ambiguity via restriction enzymes

Abstract

Publication series

Conference

Bibliographical note

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this