Web Tools for Prokaryots (''Bacteria'' and ''Archaea'') identification

Note : Prokaryotes Sequence Based Identification explains shortly what is the identification process for Bacteria and Archaea

BLAST and similarities

Databases

DDBJ (DNA Data Bank of Japan).
EBI/EMBL (Europa).
NCBI/Gen Bank (US).

GenBank BLAST

Sequences compiled as a set of words.
Recognizing a word in the sequence.
Extension from words = Open-Extend gap parameters.
Pairwise alignment and similarities.
Web site.

Limitations

No consensus to similarities level.
Identification level :
- genes and genus dependant.
- depending of the sequence submitted.
BLAST parameters are modifying the result.

Databases and integrated tools

RIDOM

Collaborative database, Type Strains.
Similarity search and phylogeny.
Trace chromatograms comparison.
Web site.
rather small database
even for clinically relevant bacteria : Nocardia experimental database gave a perfect match in 71.4\% of cases.

Microseq Applied Biosystems

Commercial database.
Blast + phylogeny.
Extended database
Web site.

BiBi (Bio-Informatic Bacteria Identification project)

A subset of Gen Bank databases (Bacteria, Archaea).
Genes used for identification
- SSU-rDNA-16S
- gyrB, recA, sodA, rpob, tmRNA, tuf, groel2-hsp65 (Actinobacteria)
Data bases are nomenclature compliant (stringent) or not (lax).
- "stringent" -> Valid published names only.
TS databases contains only TS+complete genome sequences
Combine similitude search and phylogeny.
A user friendly environment.
A set of tools to improve decision.
Web site based on a microbiologist understandable approach.

BiBi "le" (ligth edition)

Thus BIBI was more an identification environment that an automated system.
This tendancy has been emphasized, see Inside Bibi Le and Bibi Le Results to understand the evolution.

Possible future of sequence-based identification

Quality of the databases +++.
Specialized curated databases are necessary.
Use of great alignments (more than 10000 sequences).

Prokaryotes Identification Web Tools