(Q27304453)

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Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants

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scholarly article

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Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants (English)

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computational biology

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based on heuristic

inferred from title

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based on heuristic

inferred from title

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based on heuristic

inferred from title

computational benchmark

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based on heuristic

inferred from title

Akifumi S Tanabe

object named as

Akifumi S Tanabe

1

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object named as

Hirokazu Toju

2

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language of work or name

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publication date

2013

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8

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10

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e76910

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copyright license

Creative Commons Attribution 4.0 International

18 October 2013

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April 2022 Public Data File from Crossref

copyright status

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Structure, function and diversity of the healthy human microbiome

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21 March 2017

Biodiversity loss and its impact on humanity

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21 March 2017

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

BLAST+: architecture and applications

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

A DNA barcode for land plants

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

DNA barcoding the floras of biodiversity hotspots

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

MEGAN analysis of metagenomic data

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

The neighbor-joining method: a new method for reconstructing phylogenetic trees

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

BARCODING: bold: The Barcode of Life Data System (http://www.barcodinglife.org)

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

MRBAYES: Bayesian inference of phylogenetic trees

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

Estimation of fish biomass using environmental DNA

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21 March 2017

PhymmBL expanded: confidence scores, custom databases, parallelization and more

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

21 March 2017

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

7 April 2017

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

7 April 2017

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

7 April 2017

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Bioinformatic challenges for DNA metabarcoding of plants and animals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Taxonomic classification of metagenomic shotgun sequences with CARMA3.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Progress towards DNA barcoding of fungi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Comparative performances of DNA barcoding across insect orders

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

DNA barcoding for ecologists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

A universal DNA mini-barcode for biodiversity analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring

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28 September 2017

DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

DNA barcoding will often fail to discover new animal species over broad parameter space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

The perils of DNA barcoding and the need for integrative taxonomy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

28 September 2017

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

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28 September 2017

Community composition of root-associated fungi in a Quercus-dominated temperate forest: "codominance" of mycorrhizal and root-endophytic fungi

1 reference

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31 May 2018

Taxonomic metagenome sequence assignment with structured output models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3799923

31 May 2018

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

Surveillance of fish species composition using environmental DNA

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

Statistical assignment of DNA sequences using Bayesian phylogenetics

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

A minimalist barcode can identify a specimen whose DNA is degraded

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

Testing the reliability of genetic methods of species identification via simulation.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0076910

21 January 2018

Identifiers

10.1371/JOURNAL.PONE.0076910

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2013PLoSO...876910T

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OpenCitations bibliographic resource ID

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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