Resources for community profiling

The SilvaMod and SSUrdb databases have now been updated and integrated into CREST (Classification Resources for Environmental Sequence Tags). To download the latest version, based on SILVA SSURef 106, please visit the CREST Download page.

SilvaMod v100 (2010)

This database was developed using the Silva SSURef100 and its associated taxonomy in order to otpimise the resolution and reliability of LCA classification using MEGAN [2]. All files are compressed using the ZIP format.

A 16S rRNA reference sequence database was prepared based on the Silva Taxonomy in Silva SSURef release 100. Using the ARB software package, we reviewed the SSURef alignment and removed all sequences with a pintail score below 75, alignment quality score (align_qual_slv) below 75 or length below 1,200 bp, leaving 341,683 sequences. In addition, we manually reviewed and edited Silva Taxonomy assignments with a focus on the Epsilonproteobacteria, Archaea, Acidobacteria and Chloroflexi. Further, a number of misspelled and inadvertently repeated taxon names were corrected.

Please note that this version is not compatible with the NCBI Taxonomy! In order to utilise the Silva Taxonomy in MEGAN, download the compressed file consisting of: 1) a MEGAN synonyms file (SSURef100_100309.synonyms.txt); 2) a .tre file; and 3) a .map file. These files must be loaded by MEGAN by using the commands 1) "File > Setup Import > Load Synonyms File" and to tick "Use Synonyms File" in the same menu; 2) "File > Tools > Import Taxonomy File"; and 3) In the last tab when importing blast results, by selecting "Load Synonyms File" and by checking the box "Use Synonyms File".

The identifier used for each sequence is its accession number, which is associated with a node in the NCBI Taxonomy using a lookup table distributed together with MEGAN. In order for this to work, you need to tick the option "Use Accession Lookup" under "Setup Import" in the File menu, before BLAST output data using the the reference databases, is imported. This is NOT neccessary for the new version (SSURef100 based)

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SSUrdb and LSUrdb (2008)

In [1], we extended the NCBI Taxonomy by grafting to it a number of archaeal candidate divisions, as proposed by Schleper et al [3]. The reference databases may be used without making this extension, but we have provided the files necessary, should you wish to do so. The ribosomal sequences are available in FASTA format and divided into a Small subunit SSUrdb and a Large subunit database LSUrdb.

If you have any questions about how to use this database, please contact Anders Lanzén

Downloads

References

  1. Urich, T.; Lanzén, A.; Qi, J.; Huson, D.H.; Schleper, C.; Schuster, S. (2008), 'Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transciptome', PLoS ONE 3(6): e2527 doi:10.1371/journal.pone.0002527.

  2. Huson, D. H.; Auch, A. F.; Qi, J. & Schuster, S. C. (2007), 'MEGAN analysis of metagenomic data.', Genome Res 17(3), 377--386.

  3. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3: 479-488.