In microbiome analyses, often rRNA gene databases are used to assign taxonomic names to sequence reads.
The TaxMan server facilitates the analysis of the taxonomic distribution of your reads in two ways.
First, you can check what taxonomic names are assigned to the sequences produced by your primers and what taxa you will lose.
Second, the produced amplicon sequences with lineages in the FASTA header can be downloaded.
This can result in a much more efficient analysis with respect to run time and memory usage,
since the amplicon sequences are considerably shorter than the full length rRNA gene sequences.
In addition, you can download a lineage file that includes the counts of all taxa for your primers and for the used reference.
We have preprocessed the databases so that they now all include the taxonomic lineage in the FASTA header.
For references and links to the databases, see below.
Documentation:
Please cite TaxMan and the reference dataset you used:
Brandt, B.W., Bonder, M.J., Huse, S.M. and Zaura, E. (2012)
TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage.
Nucleic Acids Research 40:W82-W87.
Databases:
CORE:
Griffen, A.L., Beall, C.J., Firestone, N.D., Gross E.L., DiFranco, J.M., Hardman, J.H., Vriesendorp, B., Faust, R.A., Janies, D.A. and Leys, E.J. (2011)
CORE: A phylogenetically-curated 16S rDNA database of the core oral microbiome.
PLoS ONE 6(4): e19051.
HITdb:
Ritari, J., Salojärvi, J., Lahti, L., de Vos, W.M. (2015)
Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database.
BMC Genomics 16(1):1056.
HOMD:
Chen, T., Yu, W-Han, Izard, J., Baranova, O.V., Lakshmanan, A., Dewhirst, F.E. (2010)
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
Database, Vol. 2010
Database 2010:baq013.
Greengenes:
DeSantis, T. Z., Hugenholtz P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber T.,Dalevi, D., Hu, P. and Andersen, G.L. (2006)
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
Applied and Environmental Microbiololgy 72(7):5069-5072.
SILVA:
Pruesse, E., Quast, C., Knittel, K., Fuchs, B., Ludwig, W., Peplies, J. and Glöckner, F.O. (2007)
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Nucleic Acids Research 35(21):7188-7196.
SIS: 18S-ITS1-5.8S:
Usyk, M., Zolnik, C.P., Patel, H., Levi, M.H. and Burk, R.D. (2017)
Novel ITS1 fungal primers for characterization of the mycobiome.
mSphere 2: e00488-17.
[Note: we have mapped the entire taxonomic lineages to the sequences in SIS.]
UNITE ITS:
Kõljalg, U., Nilsson, R.H., Abarenkov, K., Tedersoo, L., Taylor, A.F.S.,
Bahram, M., Bates, S.T., Bruns, T.D., Bengtsson-Palme, J., Callaghan, T.M., Douglas, B.,
Drenkhan, T., Eberhardt, U., Dueñas, M., Grebenc, T., Griffith, G.W., Hartmann, M., Kirk,
P.M., Kohout, P., Larsson, E., Lindahl, B.D., Lücking, R., Martín, M.P., Matheny, P.B.,
Nguyen, N.H., Niskanen, T., Oja, J., Peay, K.G., Peintner, U., Peterson, M., Põldmaa, K.,
Saag, L., Saar, I., Schüßler, A., Scott, J.A., Senés, C., Smith, M.E., Suija, A., Taylor, D.L.,
Telleria, M.T., Weiß, M., Larsson, K-H. (2013)
Towards a unified paradigm for sequence-based identification of Fungi.
Molecular Ecology 22(21):5271-5277.
Vaginal 16S reference package, by
Hoffman, N., Srinivasan, S. and Matsen, M.
Visualization:
jqPlot is a plotting and charting plugin for the jQuery Javascript framework.
This is used to plot the pie charts.
Dynamic HTML and our Javascript code is used for the expandable tree and for interactive plotting.
Background Reading:
Crielaard, W., Zaura, E., Schuller, A.A., Huse, S.M., Montijn, R.C. and Keijser, B.J.F. (2011)
Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health.
BMC Medical Genomics 4:22.
Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A. and Sogin, M.L. (2008)
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.
PLoS Genetics 4(11): e1000255.
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