dblast Software as a Service for rRNA-based Identification

dblast is our Software as a Service (SaaS) system for the identification of Bacteria and Fungi based on ribosomal RNA gene sequences.

Your query sequences are uploaded to a login-protected online server and immediately analysed, any search is done in less than 5 seconds. Your results can be viewed in the web interface of the system and downloaded as a pdf report for approval and archiving.

Every query sequence is searched against two comprehensive and high-quality reference databases of Bacteria and Fungi in parallel. The bacterial subset represents nearly all publicly available valid bacterial species (full length SSU rRNA). The fungal subset covers a representative subset of organisms relevant for identification in typical routine applications (D2 region of the LSU rRNA).

Main Features

  • more than 10k bacterial and 2,4k fungal reference species, respectively
  • up-to-date nomenclature and regularly updated -> identification represents current scientific status
  • integrated user management, organize your complete team
  • fully validated, used within GMP-regulated environments

The dblast service was developed for users which rely on highly reliable identification results (species level) based on ribosomal RNA gene sequence analysis. This group mainly includes clinical laboratories and quality control laboratories in industry (environmental monitoring, raw material testing, root cause analysis, etc.). But of course the service is also available to all other users interested.

The dblast reference database consist of two subsets of ribosomal rRNA gene sequences which are searched and reported in parallel for every of your query sequences:
A set of nearly all validly described bacterial species (full length 16S rRNA gene) and a set of selected fungal species of taxa relevant for diagnostics purposes (commonly used D2 region of the 28S rRNA gene).

Current status (September 2016) of the two dblast reference subsets:

Bacteria v4.0: 10.261 reference entries (species)
Fungi v2.0: 2.452 reference entries (species)

The dblast reference database follows the idea of the The All-Species Living Tree Project (LTP) of providing a single reference per validly described bacterial species, represented by only public type strain sequences.
This approach provides three major advantages:

    (i) clear identification results and assessment (due to the absence of redundancy)
    (ii) use of only original type strain sequences guarantees correctly assigned species names
    (iii) starting from the complete public repositories results in a scientifically comprehensive and up-to-date database resource

However, compared to the academic LTP project (the highest quality SILVA-related subset), the dblast reference database has been subjected to intensive additional quality management which even meets industrial GxP-requirements. This is of major importance for professional routine applications because not all publicly available type strain sequences meet the standards required.

In conclusion, the dblast solution represents a direct implementation of our mission to make available the status quo of microbial systematics for industry-grade applications (see our Company and Networking pages).


Reporting:

For maximum overview and easy approval, the dblast system does not report its results as a list of always the best n hits, but instead uses the hit list organization scheme outlined below.
In this context, the system follows the concept of a 99% sequence identity threshold for reliable rRNA gene-based microbial species identification and a 97% cut-off for genus assignment.

  • if the best hit shows 100% identity - all other hits of 100% are listed (if true) and the first hit <100%
  • if the best hit shows <100% to 99% identity - all hits of this category are shown and the first hit <99%
  • if the best hit shows <99% to 97% identity - all hits of this category are shown and the first hit <97%
  • if the best hit shows <97% identity - the best 20 hits are shown

The name dblast stands for 'diagnostic blast' and briefly describes how the tool works and what you can get out of it.

When users read 'BLAST', they usually think about the online service provided by NCBI which is mainly used to search the entire primary GenBank database, often resulting in unsatisfactory hit lists in terms of complexity and precision. Reason is the mass of redundant, incomplete and not quality-controlled information deposited by the community. But more correctly, BLAST (Basic Local Alignment Search Tool) is a generic toolbox for local installation based on a specific algorithm.

The original BLAST manuscript is one of the most-cited papers in scientific literature and since two decades the toolbox is considered to be an industry-standard workhorse. Therefore, we decided to apply selected BLAST components in the dblast core module for robust initial sequence alignment and search. However, the system does not provide a standard BLAST output to you. BLAST parameters have been optimized for rRNA gene reference databases and an advanced post-processing routine filters the BLAST output for potential invalid hits (based on partial alignments) and also categorizes the results.

In combination with the high-quality reference database (see above), the dblast system provides highly reliable species identification within the resolution capacity of the ribosomal RNA gene. This is why we decided for the extension 'diagnostic', to express the accurateness of the system.

The dblast system was developed and is operated by us under the guidelines of Computerized System Validation (CSV) and we are running dedicated instances for customers from pharmaceutical industry and regulated by GMP/GAMP requirements (Good Manufacturing Practice/Good Automated Manufacturing Practice). In terms of quality assurance and rRNA gene-based identification capacity, there is no comparable bioinformatics solution on the market. Even if you are less regulated or not officially regulated at all, your identification routine will profit from this level of quality.

The dblast system is used by one of the world's leading pharmaceutical companies within their GMP-regulated network of global quality control laboratories. All laboratories are uploading their query sequences to the same central server, gaining maximum harmonization of identification and minimum workload in terms of system maintenance and database updating.

In conclusion, a massive cost reduction, combined with significantly improved identification results because the dblast database is reflecting the current scientific status of microbial systematics, an outstanding feature in the field of industrial microbial identification.


Enquiries & Demo

For more information and enquiries related to our dblast system, please contact:

dblast@ribocon.com


On request, we also provide free access to our dedicated dblast demo system.

There you can upload (copy and paste) own query sequences and view and download your identification results. Privacy of your data is assured.

See also our Networking page for further information on the resources we rely on in terms of sequence data, taxonomy, and nomenclature in Microbiology.