A Practical and Scalable Tool to Find Overlaps between Sequences
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 prob...
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| Format: | Article |
| Language: | English |
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Hindawi Limited
2015-01-01
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| Series: | BioMed Research International |
| Online Access: | http://dx.doi.org/10.1155/2015/905261 |
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doaj-053e7caf1f984a62b928a1a70bc4f4ac2020-11-24T22:16:18ZengHindawi LimitedBioMed Research International2314-61332314-61412015-01-01201510.1155/2015/905261905261A Practical and Scalable Tool to Find Overlaps between SequencesMaan Haj Rachid0Qutaibah Malluhi1KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, QatarKINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, QatarThe 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.http://dx.doi.org/10.1155/2015/905261 |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Maan Haj Rachid Qutaibah Malluhi |
| spellingShingle |
Maan Haj Rachid Qutaibah Malluhi A Practical and Scalable Tool to Find Overlaps between Sequences BioMed Research International |
| author_facet |
Maan Haj Rachid Qutaibah Malluhi |
| author_sort |
Maan Haj Rachid |
| title |
A Practical and Scalable Tool to Find Overlaps between Sequences |
| title_short |
A Practical and Scalable Tool to Find Overlaps between Sequences |
| title_full |
A Practical and Scalable Tool to Find Overlaps between Sequences |
| title_fullStr |
A Practical and Scalable Tool to Find Overlaps between Sequences |
| title_full_unstemmed |
A Practical and Scalable Tool to Find Overlaps between Sequences |
| title_sort |
practical and scalable tool to find overlaps between sequences |
| publisher |
Hindawi Limited |
| series |
BioMed Research International |
| issn |
2314-6133 2314-6141 |
| publishDate |
2015-01-01 |
| description |
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. |
| url |
http://dx.doi.org/10.1155/2015/905261 |
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AT maanhajrachid apracticalandscalabletooltofindoverlapsbetweensequences AT qutaibahmalluhi apracticalandscalabletooltofindoverlapsbetweensequences AT maanhajrachid practicalandscalabletooltofindoverlapsbetweensequences AT qutaibahmalluhi practicalandscalabletooltofindoverlapsbetweensequences |
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