TaxMan statistics

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Associated diseases

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TaxMan specifications

Information


Unique identifier OMICS_02614
Name TaxMan
Interface Web user interface
Restrictions to use None
Input data Forward and reverse PCR primer sequence(s)Input format: FASTA
Output data Overview of the run (number of non-redundant sequences in the selected database and number of total and non-redundant sequences that the primers formed)
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TaxMan

TaxMan in publications

 (3)
PMCID: 5028031
PMID: 27643794
DOI: 10.1371/journal.pone.0163178

[…] more than 8 bp of homopolymer, and a length between 370 and 380 bp (after removal of primers and barcode sequences), since most of the expected amplicons ranged from 370 to 380 bp length (judged by taxman database; http://www.ibi.vu.nl/programs/taxmanwww/; []). chimeric sequences were removed using uchime v4.2 []. taxonomy was assigned to each read by using the rdp_trainset v14 database [], […]

PMCID: 4841035
PMID: 27102333
DOI: 10.1186/s13073-016-0295-y

[…] optimal picking, which uses uclust [], version 1.2.22q, to perform the clustering. as a reference database, we used a primer-specific version of the full greengenes 13.5 database []., using taxman [], we created the primer-specific reference database, containing only reference entries that matched our selected primers. during this process we restricted the mismatches of the probes […]

PMCID: 4596485
PMID: 26358192
DOI: 10.1161/CIRCRESAHA.115.306807

[…] sequence reads based on similarity) (version 1.2.22q) to perform the clustering. matching otus to bacteria was done using a primer-specific version of the greengenes 13.5 reference database. using taxman, we created the primer-specific reference database containing only reference entries that matched the selected primers. during this process, we restricted probe-reference mismatches […]


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TaxMan institution(s)
Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam, Amsterdam, Netherlands; VU University Amsterdam, Amsterdam, Netherlands; Centre for Integrative Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands; Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
TaxMan funding source(s)
This work was supported by the University of Amsterdam under the research priority area ‘Oral Infections and Inflammation; National Science Foundation [NSF/BDI 0960626]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446.

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