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.
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
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