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

Alberto Montañola, Concepció Roig, Porfidio Hernández

Research output: Contribution to journalArticleResearchpeer-review

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.
Original languageEnglish
Pages (from-to)251
JournalJournal of integrative bioinformatics
Volume11
Issue number3
DOIs
Publication statusPublished - 1 Jan 2014

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