leBIBI IV SSU-rDNA (16S) Automated ProKaryotes Phylogeny

The previous version (leBIBI) can no longer be maintained

The DB construction engine was written in python2.8 wich is now obsolete

The web server was also written in python 2.8

It appears that the adaptation to python3 was mandatory, but due to the age of the scripts -some being more than 10years old- it was more efficent to rebuilt a new extraction engine and a new website.

We also choose to focuse on the quality of the DB and of the phylogenetic reconstruction engine. Some formely accepted but currently questionnable solutions have been dropped.

The PPF phylogeny reconstruction engine is also obsolete is already disconnected. Note than the interrogation of BIBI IV by using #genus_species is somewhat giving a decent alternative.

The new Website engine is only working with the new BIBI DB format wich is no more usable by the former "Legacy lebibi.

The current situation

The BIBI IV replaces the previous version for SSU-rDNA (16S) phylogeny.

The leBIBI legacy website will be working as long as the computer and the softwares will accept to run the program

It will be limited to the proteins search and phylogeny as we dont have any solution up to now.

Please note that the DB is now obsolete, and the solutions used to reconstruct the phylogeny are currently questionable.

The proteins databases will not be updated after version 39 (end 2019).

Possible evolution

Maintaining many databases is work and time. We absolutely need to focuse on some databases only.

From a technical point of view, building a LSU-rDNA (23S) DB compatible with BIBI IV is possible but 23S sequences are much less abundant in the databases and the coverage is not homogenous. This lower the interest of this DB. It is currently non available.

Concerning the proteins, we hope to use the RiboDB engine to generate the databases. Unifying the processes between RiboDB and BIBI IV may a good solution to lower the burden and the BIBI IV databases construction engine is already sharing major routines with the RiboDB engine.

 

 

logo LBBE

LABORATORY OF BIOMETRY
AND
EVOLUTIONARY BIOLOGY

logo CNRS logo university

Original solution copyright w3schools.com