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

Author
Comin, M.; Farreras, M.
Type of activity
Presentation of work at congresses
Name of edition
20th European MPI Users' Group Meeting
Date of publication
2013
Presentation's date
2013-09
Book of congress proceedings
Proceedings of the 20th European MPI Users' Group Meeting (EuroMPI 2013): Madrid, Spain: September 15-18, 2013
First page
211
Last page
216
Publisher
ACM
DOI
https://doi.org/10.1145/2488551.2488579 Open in new window
Project funding
Computación de altas prestaciones V: arquitecturas, compiladores, sistemas operativos, herramientas y aplicaciones
Repository
http://hdl.handle.net/2117/22471 Open in new window
URL
http://dl.acm.org/citation.cfm?id=2488579 Open in new window
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 suit...
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.
Keywords
Parallel algorithms, Suffix tree, Whole genome indexing
Group of research
CAP - High Performace Computing Group

Participants

  • Comin, Matteo  (author and speaker )
  • Farreras Esclusa, Montserrat  (author and speaker )