Limits...
A Practical and Scalable Tool to Find Overlaps between Sequences.

Rachid MH, Malluhi Q - Biomed Res Int (2015)

Bottom Line: The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure.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.

View Article: PubMed Central - PubMed

Affiliation: KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, Qatar.

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.

No MeSH data available.


Related in: MedlinePlus

Finding all-pairs suffix-prefix.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4417569&req=5

alg3: Finding all-pairs suffix-prefix.

Mentions: If local_position is greater than the chain_len of the current node, then current_node should point to the appropriate branch which is labeled by c, where c is the current character to be compared in Suij. If no such branch exists, then Suij does not represent any suffix-prefix match.


A Practical and Scalable Tool to Find Overlaps between Sequences.

Rachid MH, Malluhi Q - Biomed Res Int (2015)

Finding all-pairs suffix-prefix.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4417569&req=5

alg3: Finding all-pairs suffix-prefix.
Mentions: If local_position is greater than the chain_len of the current node, then current_node should point to the appropriate branch which is labeled by c, where c is the current character to be compared in Suij. If no such branch exists, then Suij does not represent any suffix-prefix match.

Bottom Line: The paper demonstrates an efficient construction of this time-efficient and space-economical tree data structure.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.

View Article: PubMed Central - PubMed

Affiliation: KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, Qatar.

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.

No MeSH data available.


Related in: MedlinePlus