Release information: SILVA 108

Release 108 of the SSU and LSU databases as released on 01. September 2011

 

SSU 108 LSU 108
Parc

2,492,653

(+ 529,701)

269,440

(+ 37,884)

Ref 618,442

(+ 62,912  )

23,600

(+ 2641)

HSM/

MWM

402,021

(+ 145,555)

Human skin microbiome

Mouse wound microbiota

 

Former statistics:

SILVA 94, SILVA 95, Silva 96, SILVA 98, SILVA 100

SILVA 102 , SILVA 104, SILVA 106

Small Subunit rRNA Database

SSU Parc (Web database & ARB file) contains all aligned sequences with an alignment quality value, a basepair score or a sequence quality equal and above 30. All sequences with a Pintail value < 50 or an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). No further sequence curation has been applied.

To create SSU Ref (Web database & ARB file), additionally, all sequences below 1,200 bases for Bacteria and Eukarya and below 900 bases for Archaea or an alignment quality value below 50 have been removed from SSUParc. A guide tree was calculated by adding all sequences to the tree_1200 of SILVA release 106 which is based on tree_1000 from the ssujan04 release. For tree calculation, highly variable positions were removed for Bacteria, Archaea, and Eukarya with the respective position variability filters. The tree for Bacteria and Archaea have been organized mainly based on the Bergey's taxonomic outline, LPSN and the literature. After manually inspection of the tree, some sequences have been removed due to long branches. Position variability filters for Bacteria, Archaea and Eukarya have been calculated and added to the dataset.  All sequences with a Pintail value < 50 or an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). Before using the alignment for extensive phylogenetic reconstructions all sequences should be checked carefully.

Large Subunit rRNA Databases

LSU Parc (Web database & ARB file) contains all aligned sequences with an alignment quality value, a basepair score or a sequence quality equal and above 30. All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). No further curation has been applied.

Additionally, for LSU Ref (Web database & ARB file) all sequences below 1,900 bases have been removed, a guide tree was calculated based on the tree_1900 of SILVA release 106, and basic filters have been added. The tree for Bacteria and Archaea have been organized mainly based on the Bergey's taxonomic outline, LPSN and the literature. All sequences with an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). Please take into account that the SEED consisted only of around 2,800 sequences and there is no guaranty that well aligned close relatives have always been available. We would recommend additional manual curation before using it for extensive phylogenetic reconstructions.

Taxonomies, Names, Type Strain & Genome Information

Taxonomy

With SILVA release 102 the default taxonomy shown on the webpage (browser/search) is the SILVA taxonomy. At the this is only available for the sequencs that are part of the Ref(erence) datasets (SSU & LSU). To show the classification of all sequences (Parc) in the SILVA databases you have to switch to EMBL taxonomy.  

Alternative Taxonomies

Besides the SILVA and EMBL taxonomy, alternative classifications taken from the greengenes and the RDP II project are also available in SILVA. On the webpage, the user can switch using the taxonomy menu. In ARB, the different taxonomies can be found in the fields: tax_slv, tax_embl, tax_gg and tax_rdp for SILVA, EMBL, greengenes and RDP II, respectively. The corresponding *_name fields shows the respective sequence name for each entry.  Please take into account that both greengenes and RDP II provide only a subset of the sequences hosted by SILVA. If no taxonomic mapping to greengenes or RDP II was available they are assigned as "unclassified" and the respective sequence name equals EMBL. For the LSU datasets only SILVA and EMBL taxonomies are available.

Altenative Names

All names of validly described species in the SSU and LSU databases have been checked for changes (basonyms, synonyms and orthographical corrections) against the DSMZ "Nomenclature up to date" catalogue (Opens external link in new windowhttp://www.dsmz.de/download/bactnom/names.txt) released in June 2011.

Cultured and Type strains

The information if a sequence originates from a cultured or type strain has been added to the field strain and is indicated by [T] and [C]. Several sources have been used to compile the information: The Opens external link in new windowStrainInfo.net bioportal, The Ribosomal Database Project II (10.26) and the Living Tree Project which provides manually curated information compliant with Euzebys "Opens external link in new windowList of Prokaryotic names with Standing in Nomenclature".

Genomes

The information if a sequence originates from a genome project has been taken from Opens external link in new windowEMBL and added to the field strain. It is indicated by e[G].

 

Detailed information about the corresponding identifiers and target databases can be found in the table to the right.

The identifiers can be used for data retrieval by searching in the strain field see Opens internal link in current windowFAQ.

Quality Values

The length and colours of the bars give a first indication on the sequence and alignment quality as well as the risk for sequence anomalies based on Pintail analysis. After downloading the sequences as an ARB file, sequences that need attention can be selected by searching for low quality (alignment, sequence) or Pintail values in the corresponding ARB database fields. A full description of the colour code and all database fields available in the ARB files can be found in the Opens internal link in current windowFAQ section. Taking into account the rich set of sequence associated information that comes along with every SILVA sequence, user designed sub-databases can be easily generated.

SEED

All rRNA sequences have been aligned based on a completely manually re-checked SEED alignment of 57,445 rRNA sequences for SSU and 2,868 rRNA sequences for LSU. The SSU alignment is based on the official ssu_jan04 release of the ARB Project. The SSU SEED alignment has been considerably improved for Archaea by manual addition of more than 1,000 sequences by Katrin Knittel. All SSU Eukaryotic sequences (18S) have been cross-checked by Wolfgang Ludwig before their addition to the SEED. Most of the bacterial sequences have also undergone a curation process carried out by the SILVA Team. We would rate our SSU SEED alignment for all Bacteria and Archaea as good and for Eukarya as reasonable.

The LSU alignment was provided by Wolfgang Ludwig and has not been released before SILVA. It was cross-checked by the SILVA Team before using it as the SEED for automatic alignment.  Bacteria and Archaea could be rated as good. The Eukaryotes need definitely further attention.

Statistics

Sequence Retrieval and Processing

SSU 108 LSU 108
candidates (total) 4,301,517 779,857
RNAmmer42,6318191
< 300 bases 1,291,577 436,016
> 2% ambiguities 14,868 4086
> 2% homopolymers 6136 5605
> 2% vector contamination 2704 337
rejected by SINA 177,668 41,694

sequence or alignment quality or bp score < 30

21,926

10,739

Sequences have been retrieved from EMBL Opens external link in new windowRelease 108 (June 11) using a complex keyword search procedure and sequence based search with Opens external link in new windowRNAmmer profiles. Cross checks with RDP II indicated no loss of primary data. Most of the sequences rejected by the new SINA aligner were classified as not ribosomal RNA sequences by manual inspection or the remaining aligned sequence fragments were below 300 bases.

1. Growth of the ribosomal RNA databases since 1992


Blue: RDP II, orange: SILVA SSUParc based on the EMBL release 108

2. Length Distribution (SSU & LSU)

Red: raw data, black: the quality checked & aligned SSUParc sequences

Red: raw data, black: the quality checked & aligned LSUParc sequences

Basic statistics for the SILVA databases

    SSUParc   SSURef   LSUParc   LSURef  
Version   108   108   108   108  
Total   2,492,653   618,442   269,240   23,600  
Bacteria   2,195,477   530,197   26,230   14,692  
Archaea   87,193   25,658   362   345  
Eukaryota   187,680   62,587   242,648   8563  
Cultured #   33,842   27,163   17,582   4926  
Typestrains #   18,548   16,563   7829   2878  
                   
# according to   straininfo.net   and the Living   Tree   Project  

Strain Identifiers

Source Information Tag Datasets
EMBL Typestrains (t) SSU, LSU
EMBL Genomes e[G]  SSU, LSU
Straininfo.net Cultured s[C] SSU, LSU
Straininfo.net Typestrains s[T] SSU, LSU
Living Tree Project  Typestrains (curated)  l[T] SSU
RDP II Typestrains r[T] SSU

RNAmmer

RNAmmer is a computational predictor for the major rRNA species (SSU, LSU) from all three domains of life. The program uses hidden Markov models trained on data from the European ribosomal RNA database project. SILVA runs the profiles of RNAmmer on all sequence entries of the EMBL archive to complement the existing predictions. All predictions are marked with RNAmmer in the ann_src_field. More information about RNAmmer can be found in the Opens external link in new windowpaper.

New in Release 108

  • Webpage
    • TestProbe 2.2 is now online
    • The SINA alignment service has been significantly improved. Now available are:
      • search for similar sequences
      • sequence classification based on LCA
      • upload of up to 500 sequences
    • Improved jobmanager and job distribution on the cluster
  • ARB files
    • The 402,021 full length (Ref) sequences of the Human skin microbiome (HSM) and Mouse wound microbiota (MWM) projects have been separated from the SSURef dataset.
  • Pipeline
    • Revised quality management
      • all sequences have to pass the aligner first
      • ambiguities and homopolymers are now only counted for the rRNA gene
      • vector contamination now only counts outside the rRNA gene
      • sequences are now rejected if they have more than 2% vector contamination (before 5%)
  • Eukaryotic Taxonomy
    • is now again taken from EBI-ENA

Known Bugs

  • SSUParc: 6839 sequences have no Pintail values

Update Files

Update files are not longer provided. Because of the constant improvement we do on the SILVA pipeline we recommend to always take the latest version of SILVA and update it with your personal sequences. The difference between SILVA and your own database can be easily determined using the Opens internal link in current windowARB Merge Tool.

Future Developments

Similarity based search functionalities are planned for mid of 2008