7194 Nucleic Acids Research, 2007, Vol. 35, No. 21 SILVA SSU Ref database contains roughly the same amount of bacterial and archaeal sequences as greengenes (12) [SILVA: 165 928, greengenes: 165 759 (July 2007)] Furthermore, SILVA contains 2423 more nearly full length sequences for Bacteria than RDP II (163 505, release 9.52) (11). This is surprising considering SILVA’s less frequent release cycle (currently synchronized with major EMBL releases); one would thus anticipate SILVA to contain fewer sequences. This may have been due to a higher sensitivity in SILVA’s search and alignment protocol. Diﬀerent quality control mechanisms should not have a signiﬁcant inﬂuence, since only nearly full length sequences have been taken into account for this comparison. With this respect it has to be emphasised that the primary intention of the SILVA project is not to oﬀer the biggest database by size but more importantly to provide reliable rRNA datasets with a robust set of processing and quality values assigned to each sequence. Such quality values enable users to easily evaluate sequences in order to create subsets of sequences for speciﬁc applications, or to extract the sequences that need further attention with respect to sequence and/or alignment quality or anomalies. The alternative taxonomies and type strain information, as well as the latest nomenclature, will facilitate the daily work ﬂow of diversity analysis using classical clone based and high throughput sequencing approaches. Additionally, SILVA provides two LSU databases to support the increasing use of molecular markers with a higher resolution than the SSU rRNA (13). A taxonomic breakdown of the LSU Parc database contents showed that already 91% of the sequences are of eukaryotic origin. Alignment and aligner The current SILVA alignment is based on 46 000 and 150 000 alignment positions for the small and large subunit rRNA, respectively. The reasons for the large amount of alignment positions are: (i) large insertions often present in Eukarya and (ii) sequencing errors, such as additional artiﬁcial bases often found in homopoly- meric sequence stretches. Such errors are common and require placement to be ﬁltered before phylogenetic tree reconstruction, without corrupting the rest of the alignment. In the ‘align-to-seed’ approach implemented in the SILVA system, well aligned sequences from seed datasets are used as references for new, unaligned sequences. Therefore, the quality of the ﬁnal alignment strongly depends on the accuracy of the seed alignment. To further improve the quality of the SSU and LSU seed databases a manual curation process was performed on the latest oﬃcially released ARB dataset from January 2004. The SSU seed hosts currently over 1000 unpublished sequences that primarily cover the domain Archaea. These sequences further improve the alignment in regions of the original SSU January 2004 dataset with sparse sequence coverage. In summary, the quality and consistency of all of the seed alignments is excellent. Only minor inconsistencies could not be resolved in the Eukarya. Nevertheless, the Parc datasets exceed the corresponding SSU and LSU seeds by a factor of 8 to 25. This probably indicates that not every phylum is equally represented in the seed. Hence, before using the alignments for in-depth phylogenetic analysis, the alignment of the selected sequence should be carefully checked. Problematic sequences can be easily ﬁltered out by the quality values followed by manual curation. The SILVA team highly appreciates the return of manually inspected and corrected alignments of sequence subsets for inclusion in the SILVA seed. This will allow us to further increase the quality of future alignments. To manage the deluge of data currently available in the public databases, a new aligner (SINA) has been devel- oped. Similar to existing aligners, such as the Fast Aligner implemented in ARB (8) or the NAST aligner (20), the tool uses related sequences from the reference alignment as a template. For benchmarking the performance of SINA, standard tools, such as BAliBASE (27), could not be used since they are restricted to protein sequences. Benchmark results were obtained by removing and realigning each sequence from the seed. The results were internally compared to the original alignment by counting the number of matching and non-matching columns. Overall, SINA correctly placed 99.8% of all bases in the alignment. Furthermore, 33% and 80% of all sequences tested had no, or less than 1%, alignment errors, respectively. The high accuracy was gained in extensive test runs by changing parameter sets for gap insertions/ extension parameters and family sizes combined with subsequent manual inspection of the results by expert curators. The design and implementation of SINA as individually running processes allows distributed aligning on cluster nodes. More than one sequence per second can be aligned per CPU. Future developments To account for the growing awareness in ecology that sequence information must be treated in the proper environmental context (28), emphasis was put on the retrieval of contextual (meta)information from public databases. For easy visualisation, the ‘Environment’ subsection is available in the detailed view of the browser. Additionally, basic environmental parameters, such as exact location and time of sampling as well as physical, chemical, and biological information about the sampling site, will be added in collaboration with the International Census of Marine Microbes (ICoMM), where similar eﬀorts are ongoing (http://icomm.mbl.edu/). In upcoming releases of the SILVA databases a crosslink to the genomes mapserver at http://www.megx.net (29) will allow the geographic visualization of the sequence information as long as the location is provided. The direct addition of tag sequences below 300 nucleotides as typically produced by pyrosequencing, is not currently planned for SILVA, since it is already a main objective of the ICoMM agenda (17). Sequence based search options and alignment of user provided sequences are under development for the SILVA webpage. Finally, it must be stressed that an appropriate and stable phylogenetic