leBIBI-QBPP For the impatients

The Quick Bioinformatic Phylogeny of Prokaryotes web-server a.k.a. leBIBI-QBPP a.k.a. leBIBI is exclusively devoted to phylogenetic analysis of Archaea and Bacteria using nucleic acid sequences. The BIBI-engine uses SSUrDNA (16S), LSUrDNA (23S) and some protein-coding genes of interest for Prokaryotes phylogeny. See leBIBI-QBPP website for further information.

First glimpse

  • Do not enter anything in the Query submission, do not select any option.

  • Simply press the button [Test leBIBI with an example dataset]: a SSUrDNA (16S) sequence, picked-up at random among 40 sequences of various origins will be processed.

  • In a result window:
    • The run log is displayed in the lower-left window,
    • A simplified phylogenetic tree will appear in the lower-right window.
    • When the run is over, the results will then appear in the main window: a short description of the cluster containing the Query is first displayed, then links to the Report, the phylogenetic Tree, the Alignment and the BLAST output.
  • Click on any of the links to display the corresponding results.

Try with your own data

  • Copy the sequences (in Fasta Format) in the “Query” section, or submit a list sequences.

  • Press the button [Proceed to the next step] to use the default settings in the case of 16S rDNA sequences, or select the appropriate database if you use another gene.

  • In the lower-left frame of result window, you can follow the process for your sequence or for the set of sequences you submitted.

  • For each submitted sequence, a tree will appear in the lower-right frame.

  • The results then appear in the main frame, in succession if the submission contains more than one sequence:
    • There is a short description of the cluster corresponding to one sequence,
    • and the links to the Report, the phylogenetic Tree, the Alignment and to the Blast result.

Workflow

  • The most similar sequences of a Query sequence (alone or from a submitted set) are selected from a given database and are used to reconstruct a phylogeny around the query sequence, this is done individually for each sequence of a set.

Sequence => BLAST => sequence + set of similar sequences => alignment => phylogeny => analysis of the results

  • BLAST does not select sequences on a phylogenetic basis => some sequences that are not phylogenetically close to the query may pollute the result, be cautious !

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