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Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms

Montañola, Alberto ; Roig, Concepció ; Hernández, Porfidio

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. Nowadays, researchers are aligning thousands of these sequences, creating new challenges in order to solve the problem using the available resources efficiently. Determining the efficient amount of resources to allocate is important to avoid waste of them, thus reducing the economical costs required in running for example a specific cloud instance. The pairwise alignment is the initial key step of the MSA problem, which will compute all pair alignments needed. We present a method to determine the optimal amount of memory and computation resources to allocate by the pairwise alignment, and we will validate it through a set of experimental results for different possible inputs. These allow us to determine the best parameters to configure the applications in order to use effectively the available resources of a given system.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Montañola, Alberto ; Roig, Concepció ; Hernández, Porfidio  (2014)  Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

Online-Journal: http://journal.imbio.de/article.php?aid=251
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2014/5342



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