Efficient parallel construction of suffix trees for genomes larger than main memory

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To access the full text documents, please follow this link: http://hdl.handle.net/2117/22471

dc.contributor	Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors
dc.contributor	Universitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions
dc.contributor.author	Comin, Matteo
dc.contributor.author	Farreras Esclusa, Montserrat
dc.date	2013
dc.identifier.citation	Comin, M.; Farreras, M. Efficient parallel construction of suffix trees for genomes larger than main memory. A: European MPI Users' Group Meeting. "Proceedings of the 20th European MPI Users' Group Meeting (EuroMPI 2013): Madrid, Spain: September 15-18, 2013". Madrid: ACM, 2013, p. 211-216.
dc.identifier.citation	978-846165133-7
dc.identifier.citation	10.1145/2488551.2488579
dc.identifier.uri	http://hdl.handle.net/2117/22471
dc.language.iso	eng
dc.publisher	ACM
dc.relation	http://dl.acm.org/citation.cfm?id=2488579
dc.rights	Attribution-NonCommercial-NoDerivs 3.0 Spain
dc.rights	info:eu-repo/semantics/openAccess
dc.rights	http://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.subject	Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat
dc.subject	Àrees temàtiques de la UPC::Informàtica
dc.subject	Parallel algorithms
dc.subject	Bioinformatics
dc.subject	Parallel algorithms
dc.subject	Suffix tree
dc.subject	Whole genome indexing
dc.subject	Algorismes paral·lels
dc.subject	Bioinformàtica
dc.title	Efficient parallel construction of suffix trees for genomes larger than main memory
dc.type	info:eu-repo/semantics/publishedVersion
dc.type	info:eu-repo/semantics/conferenceObject
dc.description.abstract	The construction of suffix tree for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become everyday more complex, requiring fast queries to multiple genomes. In this paper we presented Parallel Continuous Flow PCF, a parallel suffix tree construction method that is suitable for very long strings. We tested our method on the construction of suffix tree of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input string grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the Human genome in 7 minutes using 172 nodes.
dc.description.abstract	Peer Reviewed

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