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 has been working as long as the computer and its softwares have accepted to run the program. leBIBI legacy has been stopped (April 1, 2022)

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

However the DB (mk39) was obsolete, and the solutions used to reconstruct the phylogeny were currently questionable.

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.

NEW! Concerning the proteins, we are now using the RiboDB engine to generate the databases. Unifying the processes between RiboDB and BIBI IV is our solution to lower the burden and the BIBI IV databases construction engine is already sharing major routines with the RiboDB engine.

==>A FIRST PROTEIN DATABASE IS AVAILABLE and others will be integrated progressively
[What are your favorite proteins ?].

Note:The phylogeny outputs for proteins markers are non-optimally integrated in the BIBI IV engine, so the appearance of the trees may be strange (although correct) and some functions will not work as expected



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