leBIBI-NEWS

2018 Nov 26

The LSU (23S) bibi-DB can now be selected to extract 23S sequences or to reconstruct the phylogeny. The selection is given by the “Sequence Database used for the recruitment of similar sequences” option, even if you do not need a BLAST search.

2018 Oct 08

A query containing “subsp.” is now possible in PPF (like #Staphylococcus_aureus_subsp._aureus @TS-stringent %notag). It is also possible for the genus name to be followed by “sp.”, but it is much better to send the genus name alone to select the usual binominal species names.

2018 Oct 06

All the DB are now refreshed. Version 37 of the DB

2018 Oct 01

A new approach of the 16S/23S bibiDB construction has led to the release of bibiDB v37 (2018/Oct/06). The construction engine is completely rewritten.

  • Previous method:
    • Since 2003 bibiDB was using the ACNUC access to GenBank or EMBL-ENA
    • Sequences were proofed for quality and strand through BLAST
    • Names were adapted to the nomenclature during the extraction process with uncertainties
    • The reference status of a sequence were determined with help of LPSN or by the presence in RefSeq
    • Due to an heavy patching the engine was somehow unstable and becomes more and more difficult to use.
  • New approach:
    • RNAcentral: The non-coding RNA sequence database is now the source of the sequences and of most of the information
      • RNAcentral database is made of unique sequences with an unique identifier URSnnnn
        • One URS may gather multiple identical sequences
        • Positive point: No duplicates and a reduced collection of RNA
        • Positive point: Quality-Control
        • Positive point: Strand indicated
        • Negative point: identical sequences may correspond to various taxonomical levels
    • Taxonomy DB is now the EMBL-ENA taxonomy

    • The source of information concerning Type Strains sequences is now both SILVA and LPSN

    • The key point is the now the use of logical rules to give a relevant name to a sequence or a set of sequences sharing the same URS.

    • To speed-up the process (and finaly this will be incorporated in the leBIBI web-site engine) several ZoDB (and ZOE) databases are used.

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