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  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.
|Title of host publication||Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings|
|Editors||Roderic Guigo, Dan Gusfield|
|Number of pages||14|
|ISBN (Print)||3540442111, 9783540442110|
|State||Published - 2002|
|Event||2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy|
Duration: 17 Sep 2002 → 21 Sep 2002
|Name||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Conference||2nd International Workshop on Algorithms in Bioinformatics, WABI 2002|
|Period||17/09/02 → 21/09/02|
Bibliographical notePublisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.
ASJC Scopus subject areas
- Theoretical Computer Science
- Computer Science (all)