NDLI: Filtering algorithms for sequencing constraints: Application in physical mapping

Content Provider	IEEE Xplore Digital Library
Author	Zidoum, H.
Copyright Year	2009
Description	Author affiliation: Dpt. of Computer Science, Sultan Qaboos University - College of Science Al Khod, OMAN (Zidoum, H.)
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.
Starting Page	88
Ending Page	95
File Size	659008
Page Count	8
File Format	PDF
ISBN	9781424438075
DOI	10.1109/AICCSA.2009.5069309
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-05-10
Publisher Place	Morocco
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Filtering algorithms Probes Cloning Sequences DNA Genomics Bioinformatics Data structures Labeling Application software
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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