Optimizing Multiple Pairwise Alignment of Genomic Sequences in Multicore Clusters

Autor:	Concepció Roig, Porfidio Hernández, Alberto Montañola
Rok vydání:	2014
Předmět:	Multi-core processor Multiple sequence alignment Computer science business.industry Computation Message passing Cloud computing computer.software_genre Set (abstract data type) Shared memory Key (cryptography) Data mining business computer
Zdroj:	8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014) ISBN: 9783319075808 PACBB
DOI:	10.1007/978-3-319-07581-5_15
Popis:	Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. 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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_________::df663d71ca23cb1c2b3fd3b77141ffcd https://doi.org/10.1007/978-3-319-07581-5_15 Zobrazit plný text záznamu