7192 Nucleic Acids Research, 2007, Vol. 35, No. 21 Table 3. Description of database ﬁelds in ARB ﬁles exported from SILVA for SILVA speciﬁc ﬁelds and entries ARB ﬁeld name align_bp_score_slv align_cutoﬀ_head_slv align_cutoﬀ_tail_slv align_family_slv align_log_slv align_quality_slv aligned_slv ambig_slv homop_slv homop_events_slv nuc_gene_slv pintail_slv alternative_name_slv seq_quality_slv tax_gg tax_gg_name tax_rdp tax_rdp_name vector_slv Description Calculates the number of bases in helices in the aligned sequence taken into account canonical and non canonical basepairing. The cost matrix is taken from ARB Probe_Match (8) Unaligned bases at the beginning of the sequence Unaligned bases at the end of the sequence Names and scores of reference sequences in the alignment process Detailed aligner comments Maximal similarity to reference sequence in the seed Data and time of alignment by Silva Calculated percent ambiguities in the sequences, a maximum of 2% is allowed Calculated percentages repetitive bases with more than four bases, a maximum of 2% is allowed Absolute number of repetitive elements with more than four bases Aligned bases within gene boundaries Information about potential sequence anomalies detected by Pintail (22); 100 means no anomalies found. Synonyms or basonyms of the species according to the DSMZ ‘nomenclature up to date’ catalogue Summary sequence quality value calculated based on values from vector, ambiguities and homopolymers, 100 means very good Taxonomy mapped from greengenes Organism name in greengenes Nomenclatural taxonomy mapped from RDP II Organism name in RDP II Percent vector contamination, a maximum of 5% is allowed information from the initial quality checks to the alignment process, as well as information taken directly from the EMBL entry (Tables 1–3). Together with the search and query functionalities on the web site and in ARB, one can quickly search for problematic sequences or generate individual high or low quality sequence subsets for further processing or curation. The ARB package can be used to export sequences in various formats like EMBL, GenBank, or aligned and unaligned FASTA. Availability/Webpage The SILVA databases are available via a web-based interface at http://www.arb-silva.de. The web interface is divided into six sections: the browser, search, list, down- load, background, and FAQs pages. Download of the complete Parc and Ref datasets in ARB format is available in the download section. It is also possible to download ﬁles that gain additional sequences from new releases. Subsets of aligned sequences from the Parc dataset can be retrieved from the website. This is currently possible via two entry points: a taxonomic browser and advanced search functions. After selecting a database and the desired taxonomy in the browser, the user can navigate through the taxonomy by clicking on the respective nodes. A cart system is used to easily select subsets of single sequences, complete groups or even phyla. The cart system keeps the selections for the SSU and LSU databases distinct. This allows the user to select sequences from both databases simultaneously without mixing the two sequence types. However, it must be noted that any misclassiﬁcation or erroneous information provided by INSDC is currently propagated on the SILVA webpage. Additionally, the advanced search functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database ﬁelds using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. Before download, the search results must be added to the ‘List’. This can be done by either manually selecting the sequences by mouse click or by clicking on ‘Add complete result to List’ to mark and transfer all results. The coloured bars on the search page and in the short and detailed sequence views of the browser given a fast overview of the diﬀerent quality aspects assigned to every sequence. The length of the bars is a graphical representa- tion of the respective quality value. The colours classify the information into four categories: A green bar represents a value equal to or greater than 75. Yellow bars stand for values equal to or greater than 50 but less than 75. Values less than 50 are expressed by an orange bar. Red bars are only used for scores of 0. Since ‘problematic’ sequences, sequences of inadequate quality, as well as insuﬃciently aligned sequences were discarded from the databases only the Pintail scores can have 0. In the ‘List’ section of the website, the entries can be inspected, items can be deleted, and the download ﬁles can be created. By clicking on the ‘generate download’ button the user will be asked whether he would like to download the sequences as a multi-FASTA or ARB ﬁle from the download section of the web page. All generated ﬁles will be available for download on the download page for up to 24 h. The background section of the website provides additional information about the current status of the databases, and the FAQ section describes the main steps necessary to download subsets of sequences and how to merge the retrieved ARB databases with the user’s personal ARB database.