title: A Practical and Scalable Tool to Find Overlaps between Sequences.
abstract: The evolution of the next generation sequencing technology increases the demand for efficient solutions, in terms of space and time, for several bioinformatics problems. This paper presents a practical and easy-to-implement solution for one of these problems, namely, the all-pairs suffix-prefix problem, using a compact prefix tree. The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure. The paper presents techniques for parallel implementations of the proposed solution. Experimental evaluation indicates superior results in terms of space and time over existing solutions. Results also show that the proposed technique is highly scalable in a parallel execution environment.
authors.affiliation: KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, Qatar.
authors.forename: Maan Haj
authors.initials: MH
authors.lastname: Rachid
authors.affiliation: KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, Qatar.
authors.forename: Qutaibah
authors.identifier: 0000-0003-2849-0569
authors.initials: Q
authors.lastname: Malluhi
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software