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

No abstract is available for this paper.

• Publication year

  2014

• Venue

  J. Bioinform. Comput. Biol.

• Publication date

  2014-06-26

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1142/S0219720014500139PMID 24969751
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• GNU Parallel: The Command-Line Power Tool

  2011cited by this paper
• Coordinating Computation and I/O in Massively Parallel Sequence Search

  2011cited by this paper
• On the Future of Genomic Data

  2011cited by this paper
• Evaluating BLAST Runtime Using NAS-Based High Performance Clusters

  2011cited by this paper
• Hybrid MPI/OpenMP Strategy for Biological Multiple Sequence Alignment with DIALIGN-TX in Heterogeneous Multicore Clusters

  2011cited by this paper
• TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

  2010cited by this paper
• PANGEA: pipeline for analysis of next generation amplicons

  2010cited by this paper
• BLAST+: architecture and applications

  2009cited by this paper
• The NCBI BioSystems database

  2009cited by this paper
• Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

  2009cited by this paper
• High speed bulk data transfer using the SSH protocol

  2008cited by this paper
• Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

  2007cited by this paper
• Performance Comparison of MPI-Based Parallel Multiple Sequence Alignment Algorithm Using Single and Multiple Guide Trees

  2006cited by this paper
• ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis

  2006cited by this paper
• The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

  2006cited by this paper
• Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

  2006cited by this paper
• Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB

  2006cited by this paper
• Metagenomics: DNA sequencing of environmental samples

  2005cited by this paper
• Open MPI: A Flexible High Performance MPI

  2005cited by this paper
• The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

  2004cited by this paper
• Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment

  2002cited by this paper
• The RDP-II (Ribosomal Database Project)

  2001cited by this paper
• Mathematics of microbial plasmid instability and subsequent differential growth of plasmid-free and plasmid-containing cells, relevant to the analysis of experimental colony number data.

  1994cited by this paper
• Mathematics of microbial plasmid instability and subsequent differential growth of plasmid-free and plasmid-containing cells, relevant to the analysis of experimental colony number data.

  1994cited by this paper

• Assessment of soil bacterial communities in integrated crop production systems within the Amazon Biome, Brazil: a comparative study

  2024cites this paper
• Analysis of Biological Sequence Search Performance in NoSQL Database

  2020cites this paper
• Competition with insectivorous ants as a contributor to low songbird diversity at low elevations in the eastern Himalaya

  2020cites this paper
• Porting and Optimizing G-BLASTN to the ROCm-based Supercomputer

  2020cites this paper
• Contrasting diversity of vaginal lactobacilli among the females of Northeast India

  2019cites this paper
• Lablab Purpureus Influences Soil Fertility and Microbial Diversity in a Tropical Maize-Based No-Tillage System

  2019cites this paper
• Microbial community composition in Brazilian stored diesel fuel of varying sulfur content, using high-throughput sequencing

  2017cites this paper
• Different combinations of atomic interactions predict protein‐small molecule and protein‐DNA/RNA affinities with similar accuracy

  2015cites this paper
• Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems

  2015cites this paper