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...
| Publicado en: | BioMed Research International Vol. 2015; pp. 1 - 13 |
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| Autores principales: | , |
| Formato: | equations & formulas research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
4/19/2015
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109273991&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109273991 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 4/19/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109273991 109273991 109273991 10.1155/2015/905261 109273991 ppf: 1 ppct: 12 formats: fmt: @attributes: type: P tig: atl: A Practical and Scalable Tool to Find Overlaps between Sequences. aug: au: Haj Rachid, Maan Malluhi, Qutaibah affil: KINDI Lab for Computing Research, Qatar University, P.O. Box 2713, Doha, Qatar sug: subj: Sequence Analysis Methods Technology Genome Evaluation Software Design Computer Simulation Funding Source ab: 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. pubtype: Academic Journal doctype: equations & formulas research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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