16S Classifier statistics

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16S Classifier specifications

Information


Unique identifier OMICS_10244
Name 16S Classifier
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Input can be complete 16S rRNA gene or a selected hypervariable region or a combination of multiple hypervariable regions. The input file must be single line nucleotide sequences in fasta format with a '.fasta' extension and the primers should be removed from the sequences before submission.
Operating system Unix/Linux, Windows
Programming languages Perl, R
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Vineet K. Sharma <>

Information


Unique identifier OMICS_10244
Name 16S Classifier
Interface Web user interface
Restrictions to use None
Input data Input can be complete 16S rRNA gene or a selected hypervariable region or a combination of multiple hypervariable regions. The input file must be single line nucleotide sequences in fasta format with a '.fasta' extension and the primers should be removed from the sequences before submission.
Programming languages Perl, PHP, R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Vineet K. Sharma <>

Publication for 16S Classifier

16S Classifier in publications

 (8)
PMCID: 5717032
PMID: 29250053
DOI: 10.3389/fmicb.2017.02377

[…] units (otus) were clustered at the 97% similarity level using uparse version 7.1 (). final otus were generated based on the clustering results, and taxonomic assignment was performed with the rdp 16s classifier ()., statistical analysis of otu richness via good’s coverage, chao1, and shannon’s index was performed with mothur (version 1.22.2; ). one-way analysis of variance (anova) followed […]

PMCID: 5409056
PMID: 28453559
DOI: 10.1371/journal.pone.0176716

[…] uparse [] with de novo otu picking method. final otus were generated based on the clustering results, and taxonomic annotation of individual otus was based on representative sequences using rdp’s 16s classifier 2.5 and the associated training set published with this version []. to control variation resulting from an unequal number of sequences across samples, sequence resampling was performed […]

PMCID: 4976105
PMID: 27551678
DOI: 10.3389/fnut.2016.00026

[…] available and are based on different principles, such as k-mer count [sina (), rdp bayesian classifier ()], multiple sequence alignment [nast ()], blast [tuit ()], and machine learning algorithms [16s classifier ()], among others. although new algorithms continue to be developed, the rdp bayesian classifier remains the most widely used tool for taxonomic assignment of 16s sequences; […]

PMCID: 4628106
PMID: 26583008
DOI: 10.3389/fmicb.2015.01205

[…] unpublished results) at the 97% similarity level. a final total of 3091 otus were generated, and taxonomic annotations were assigned to each otu’s representative sequence by rdb’s naïve bayesian 16s classifier (; ). in summary, the classifier compares a sequence to a random subset of a data base consisting of all possible eight-base subsequences (words). each sequence is classified 100 times […]

PMCID: 4472414
PMID: 26084274
DOI: 10.1186/s12866-015-0450-4

[…] [] at a 97 % similarity level. final otus were generated based on the clustering results, and taxonomic annotation of individual otus were achieved based on representative sequences using rdp’s 16s classifier 2.5 []., to determine the significance of differences among microbial communities, three different complementary non-parametric analyses for multivariate data were used: analysis […]


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16S Classifier institution(s)
MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh, India
16S Classifier funding source(s)
This work was supported by the intramural funding received from Indian Institute of Science Education and Research Bhopal (IISER Bhopal).

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