Abstract
The physical mapping is a crucial tool in the analysis of the genomic sequences. Algorithms for the mapping process are based on NP-complete combinatorial optimizations. The problem of reconstructing the probe order is equivalent to the Consecutive Ones problem. PQ-trees have been extensively used as a suitable data structure to test the Consecutive Ones Property (COP) in the hybridization matrix. This paper presents PQR-trees, an extension of PQ-trees. PQR-trees can advantageously handle partial order information on probes. Moreover, we embed PQR-trees in the more general framework of Constraint Programming (CP). CP is an emergent software technology for declarative description and effective solving of large, particularly combinatorial, problems. We introduce Sequences a new data structure in CP and present filtering algorithms for checking the consistency of sequence constraints based on PQR-trees. We present a canonical form that characterizes a family of sequential arrangements of a given set. The relations we are dealing with are classical sets relations ∈, ⊂, ≠, = besides sequencing relations such as group, order, and metric constraints. The filtering algorithms are based on incremental consistency techniques used to reduce the PQR-trees and hence, prune the inconsistencies before the labeling phase. We claim that the sequence structure introduces a flexibility criterion on CP which renders it a suitable tool for solving NP-complete combinatorial optimizations such as physical mapping problem.
Original language | English |
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Title of host publication | 2009 IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2009 |
Pages | 88-95 |
Number of pages | 8 |
DOIs | |
Publication status | Published - 2009 |
Event | 7th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA-2009 - Rabat, Morocco Duration: May 10 2009 → May 13 2009 |
Other
Other | 7th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA-2009 |
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Country | Morocco |
City | Rabat |
Period | 5/10/09 → 5/13/09 |
ASJC Scopus subject areas
- Computational Theory and Mathematics
- Computer Science Applications
- Electrical and Electronic Engineering