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 |
|---|---|
| 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 |
|---|---|
| Country | Morocco |
| City | Rabat |
| Period | 5/10/09 → 5/13/09 |
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ASJC Scopus subject areas
- Computational Theory and Mathematics
- Computer Science Applications
- Electrical and Electronic Engineering
Cite this
Filtering algorithms for sequencing constraints : Application in physical mapping. / Zidoum, Hamza.
2009 IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2009. 2009. p. 88-95 5069309.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Filtering algorithms for sequencing constraints
T2 - Application in physical mapping
AU - Zidoum, Hamza
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=70349898406&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70349898406&partnerID=8YFLogxK
U2 - 10.1109/AICCSA.2009.5069309
DO - 10.1109/AICCSA.2009.5069309
M3 - Conference contribution
SN - 9781424438068
SP - 88
EP - 95
BT - 2009 IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2009
ER -