Downloading fasta file from silva

SILVA Taxonomy and Classifications

Every sequence in the SILVA databases carries the ENA-EBI (EMBL) taxonomy assignment. Where available, the greengenes, RDP andd LTP taxonomies are added for comparison. The ENA (EMBL) taxonomy is retrieved simultaneously with the sequences, whereas the other taxonomies are assigned to the sequences based on accession numbers. For LSU rRNA sequences no additional up to date taxonomies are available.

For the SSU and LSU Ref(erence) databases guide trees are reconstructed. The trees are incrementally built using the ARB parsimony tool with filters to remove highly variable positions. Based on the guide trees, all phylogenetic assignments are manually curated.

The taxonomy for Bacteria and Archaea divisions are organized taking into account taxonomic information provided by Bergey’s Manual of Systematic Bacteriology (volumes 1 through 4), Bergey's Taxonomic Outlines (volume 5), and the List of Prokaryotic names with Standing in Nomenclature (Euzeby ) to supplement the Bergey’s resources with the latest information of validly described bacterial and archaeal taxa. Although we are conservative in which taxa to represent, and give the priority to valid taxa, we also include Candidatus, and names without standing in nomenclature. Furthermore, extensive effort is spent to represent prominent uncultured, environmental clades. The majority of these clades are annotated in the guide tree for the SSU Ref dataset based on literature surveys and personal communications. Taxonomic groups consisting only of sequences from uncultured organisms are named after the clone sequence submitted earliest. The taxonomic paths are standardized to six ranks; Domain, Phylum, Class, Order, Family and Genus. Only taxa that are exceptions to this rule are Myxococcales, which has suborders; and Thermomicrobia, which has subclass and suborder ranks. More information about the SILVA and LTP taxonomic frameworks can be found in the respective paper.

With SILVA release the eukaryotic taxonomy has been significantly improved as part of the ETWG project. Since SILVA is now part of the UniEuk project we will adapt the Eukaryotic taxonomy as soon as the UniEuk experts have released the first version.

With SILVA release the Genome Taxonomy Database (GTDB) has been adopted. As a consequence of our efforts the following groups were prone to significant adaptations: Archaea, Enterobacterales, Deltaproteobacteria, Firmicutes, Clostridia. Betaproteobacteriales (formerly known as Betaproteobacteria) is now Burkholderiales, an order of Gammaproteobacteria. Epsilonproteobacteria vanishes within a new phylum Campilobacterota. Tenericutes are gone, they are now all part of Bacilli, inside Firmicutes.

Due to this exhaustive manual curation we believe that the SILVA rRNA databases contain the most up to date and detailed bacterial and archaeal taxonomic classification.

Scanning for unknown fields is necessary when you open your custom ARB database for the first time. The reason is that the SILVA database contains much more information assigned to each sequence than the original ARB databases. Please do the following steps:

• Start ARB with your database
• Go to Species -> Search and Query
• When the Search and Query window pops up click on Search and select one sequence in the Hitlist
• The Species Information window should pop up. Go to Fields and click on Scan unknown fields. An extended set of Databases fields should now be visible.

• Start ARB and click on Merge Two ARB Databases in the ARB Intro window
• Select Database I (source db) and Database II (target db) in the directories fields
• Click on Go
• The ARB Merge window pops up
• To make sure that the name fields are unique and synchronized in both databases click on Check Names
• When the Synchronize Names window appears, Rename Database I and II!!
• Click on Transfer Species
• Search for entries in the left database (I) you would like to transfer to the right database (II) using the Query menu
• All db entries you would like to transfer should now be shown in the Hitlist
• Click on Transfer Listed Species - Delete Duplicates in DB II
• Click on Close
• Click on Save Whole DB II or Save Changes of DB II as
• To see your new sequences in the guide tree, you have to add them first using the Parsimony 'Quick add' procedure in ARB

Show differences: The combination of Search species that don't match the query with no search string in the search field name shows all the sequences in the Hitlist which are different between DB I and DB II.

Preserve Alignment: No. Tick this box only in case the sequences in the two databases have different alignments and ARB should try to adjust the alignments according to a reference species which must be part of both databases while transferring the sequences.

If you encounter the error message Key ‘version’ exists, but has different "type" when merging two ARB databases, you need to change the "type" of a field in ARB using "convert fields" (next to where you can add/remove fields). It is disabled by default, so first "toggle expert mode". Unfortunately, ARB isn't very communicative regarding which fields have the wrong type. The "start" field is a recurring problem, as it was a "string" (or text in ARB lingo) field in older databases, but is now an "integer" (rounded numerical or number) field. This error is common when merging current SILVA databases with old (outdated) ones. To avoid further problems it is highly recommended to update to one of the latest SILVA datasets. 

There were many problems with the older versions of ARB, especially with the Name- and PT-server.

The have all been solved in the new ARB releases (v 6.X).

We strongly recommend to upgrade your systems.

ARB 6.X can be freely downloaded from: www.cronistalascolonias.com.ar

If you have further questions related to ARB itself, have a closer look at our ARB Support section.

Here, the following issues are addressed:

• ARB on Mac OS X
• ARB FAQs
• ARB Mailing List
• ARB Bug Tracker
• Professional ARB/SILVA support