INTRODUCTION — Some New Results and Tools for Protein Function Prediction, RNA Target Site Prediction, Genotype Calling, Environmental Genomics, and More

Wong, Limsoon

doi:10.1142/s021972001100580x

Cited by 3 publications

(2 citation statements)

References 15 publications

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“…In a future work, we intend to expand our optimization of nucleotide sequence search to protein sequence search, in order to improve the performance of protein function prediction for environmental genomics data. 30 For NCBI-TaxCollector, a further improvement to use multiprocessor and/or multicomputer parallelism is possible to be implemented, since the taxonomic attachment for one input line is independent from another. For MPIblastn implementation, due to variations in the size of sequences and consequently in the workload size by process, new job scheduling strategies may be implemented to handle such problems.…”

Section: Discussionmentioning

confidence: 99%

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MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment

Dias

Xavier

Rossi

et al. 2014

J. Bioinform. Comput. Biol.

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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.

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Section: Discussionmentioning

confidence: 99%

“…Our planet is populated by a large number of microbial cells (about 10 30 ), 1 most of them still remain uncultivable. 2 New sequencing technologies have allowed the studies on diversity and abundance of environmental microbiota.…”

Section: Introductionmentioning

confidence: 99%