Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem
Joint Authors
Malluhi, Qutaibah
Abouelhoda, Mohamed
Haj Rachid, Maan
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-04-16
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
The all-pairs suffix-prefix matching problem is a basic problem in string processing.
It has an application in the de novo genome assembly task, which is one of the major bioinformatics problems.
Due to the large size of the input data, it is crucial to use fast and space efficient solutions.
In this paper, we present a space-economical solution to this problem using the generalized Sadakane compressed suffix tree.
Furthermore, we present a parallel algorithm to provide more speed for shared memory computers.
Our sequential and parallel algorithms are optimized by exploiting features of the Sadakane compressed index data structure.
Experimental results show that our solution based on the Sadakane’s compressed index consumes significantly less space than the ones based on noncompressed data structures like the suffix tree and the enhanced suffix array.
Our experimental results show that our parallel algorithm is efficient and scales well with increasing number of processors.
American Psychological Association (APA)
Haj Rachid, Maan& Malluhi, Qutaibah& Abouelhoda, Mohamed. 2014. Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem. BioMed Research International،Vol. 2014, no. 2014, pp.1-11.
https://search.emarefa.net/detail/BIM-495317
Modern Language Association (MLA)
Haj Rachid, Maan…[et al.]. Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem. BioMed Research International No. 2014 (2014), pp.1-11.
https://search.emarefa.net/detail/BIM-495317
American Medical Association (AMA)
Haj Rachid, Maan& Malluhi, Qutaibah& Abouelhoda, Mohamed. Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-11.
https://search.emarefa.net/detail/BIM-495317
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-495317