{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,19]],"date-time":"2024-09-19T15:32:54Z","timestamp":1726759974617},"reference-count":21,"publisher":"World Scientific Pub Co Pte Lt","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,6]]},"abstract":" Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and ScalaBLAST. In our best case, MPI-blastn was able to run 408 times faster in 384 cores. Our evaluations demonstrated that NCBI-TaxCollector is able to perform taxonomic attachments 125 times faster and needs 120 times less RAM than the previous TaxCollector. Through our optimizations, a multiple sequence search that currently takes 37 hours can be performed in less than 6 min and a post processing with NCBI taxonomic data attachment, which takes 48 hours, now is able to run in 23 min. <\/jats:p>","DOI":"10.1142\/s0219720014500139","type":"journal-article","created":{"date-parts":[[2014,3,26]],"date-time":"2014-03-26T07:04:52Z","timestamp":1395817492000},"page":"1450013","source":"Crossref","is-referenced-by-count":8,"title":["MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment"],"prefix":"10.1142","volume":"12","author":[{"given":"R.","family":"Dias","sequence":"first","affiliation":[{"name":"Department of Microbiology and Cell Science, University of Florida, Florida, United States"}]},{"given":"M. G.","family":"Xavier","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"F. D.","family":"Rossi","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"M. V.","family":"Neves","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"T. A. P.","family":"Lange","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"A.","family":"Giongo","sequence":"additional","affiliation":[{"name":"Faculty of Biosciences, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"C. A. F.","family":"De Rose","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Pontiphical Catholic University of Rio Grande do Sul, Porto Alegre\/RS, Brazil"}]},{"given":"E. W.","family":"Triplett","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Cell Science, University of Florida, Florida, United States"}]}],"member":"219","published-online":{"date-parts":[[2014,6,26]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1006\/plas.1994.1051"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1070633"},{"key":"rf3","volume":"13","author":"Handelsman J.","journal-title":"Nat. Res. Council. 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