Nucleic Acids Research, 2007, Vol. 35, No. 21 7191 Table 2. Description of database ﬁelds in ARB ﬁles exported from SILVA for Fields and entries imported from EMBL ARB ﬁeld name EMBL ﬁeld Description acc AC Accession number ali_xx/data sequence Sequence information author RA Reference author(s) clone FT/clone Clone from which the sequence was obtained collected by FT/collected_by Name of the person who collected the specimen collection_date FT/collection_date Date that the specimen was collected country FT/country Geographical origin of sequenced sample date DT Entry creation and update date separated by ; description DE Description full_name OS Organism species gene FT/gene Symbol of the gene corresponding to a sequence region insdc PR The International Nucleotide Sequence Database Collaboration (INSDC) Project Identiﬁer that has been assigned to the entry isolate FT/isolate Individual isolate from which the sequence was obtained isolation_source FT/isolation_source Describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived journal RL Reference location lat_lon FT/lat_lon Geographical coordinates of the location where the specimen was collected nuc_region FT source Identiﬁes the biological source of the speciﬁed span of the sequence nuc_rp RP Reference positions product FT/product Name of the product associated with the feature publication_doi RX Cross-reference DOI number pubmed_id RX Cross-reference Pubmed ID speciﬁc_host FT/speciﬁc_host Natural host from which the sequence was obtained specimen_voucher FT/specimen_Voucher An identiﬁer of the individual or collection of the source organism and the place where it is currently stored, usually an institution start FT rRNA Start of the ribosomal RNA gene stop FT rRNA Stop of the ribosomal RNA gene strain FT/strain Strain from which the sequence was obtained submit_author RL Submission authors from reference location submit_date RL Submission date from reference location tax_embl OC Organism classiﬁcation according to EMBL tax_embl_name OC Organism name taken from the classiﬁcation ﬁeld tax_xref_embl FT/db_xref Database cross-reference: pointer to related information in another database title RT Reference title version ID SV Subversion from identiﬁcation line Nomenclature All organism names have been synchronized with the ‘Nomenclature up to date’ website of the Deutsche Sammlung fu¨ r Mikroorganismen und Zellkulturen’’ DSMZ (released June 2007, http://www.dsmz.de/ download/bactnom/names.txt) in order to stay consistent with the constant renaming of validly described species according to the recommendations published in the ‘International Journal of Systematic and Evolutionary Microbiology’. All former names are stored in the database and are visible on the web page, as well as in the corresponding ﬁeld of the ARB databases (Tables 1–3). SSU and LSU rRNA databases for ARB Two types of precompiled databases for both small and large subunit ribosomal RNA sequences are available in the ARB format: the high-quality Ref databases and the comprehensive Parc databases. The Ref databases are subsets of Parc, which are exclusively comprised of nearly full length 16S/18S and 23S/28S rRNA sequences. A sequence is accepted if it is at least 1200 bases long. Additionally, sequences as short as 900 bases are included if they belong to the domain Archaea. Applying a strict cut-oﬀ at 1200 bases would result in the loss of the majority of sequences of this domain. Sequences in the LSU Ref database have to be at least 1900 bases long. For quality control, all sequences that could not be unambiguously aligned (alignment quality score <50 and <30 for SSU and LSU, respectively) were removed from the Ref databases. Both Ref databases are supplemented with a guide tree based on the full length sequence tree of the ARB Jan 04 SSU and the Ludwig LSU databases, respectively. The trees were built using the ARB parsi- mony tool with ﬁlters to remove highly variable positions. Common ﬁlters like the positional variability ﬁlters were recalculated for the Ref databases. Sequences with long branches in combination with low alignment qualities (<80) were removed from the Ref databases. The rRNA Parc databases are a collection of all quality checked and automatically aligned rRNA sequences longer than 300 bases of the aligned rRNA gene (ﬁeld ‘nuc_gene_slv’, Tables 1–3). The name Parc has been chosen according to the UniProt concept (23), where Parc stands for the comprehensive protein sequence archive. All sequences in the SILVA databases are associated with a rich set of sequence and process parameters. Included is