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Modelling DynW Rfit

Identifying BIBI webtool (Bacteria and Archaea Identification) BIBI Help and Description

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Bibi Le Results

Panorama of the results

MOST OF THIS PAGE REMAINS UP TO DATE, BUT THE TABULATED RESULTS HAVE BEEN IMPROVED. RESULTS ARE SELF EXPLICATIVE. WE HOPE TO GIVE A COMPLETE DESCRIPTION SOON.

Title line

This is to remember what we are studying. If a name (The Name) has been given, it appears here

Query : The_Name search in Bacteria_SSU-rDNA-16S_stringent

followed by the sequence Data Base corresponding to your choice.

Alignment method, base composition and length

The first line gives the alignment speed, and the tree construction option (gaps/no gaps) :

Alignment speed is set to 3 Phylogeny : tossgaps set to F -- 0 Sequence(s) complementary

In some cases the query sequence is complementary of the Data Base sequences, in other cases one or more of the Data Base sequence are complementary of the query, this is indicated here.

Tabulated results

These propositions of results are automatically generated.

Bibi Le proposes here name of the origin (species, strain) of sequences sharing a common node upward. The first table is not used up to now, only the second one is relevant.
In some cases like here :

Bibi Le proposes two (or more) results, reading the tree is mandatory.
Note that Bibi Le does not uses the distance to fill this table ! distance between the query and the node, or other sequences has to be taken into account.

Commentaries

These commentaries are automatically generated, Bibi Le is not intelligent but it tries to help you to read the tree and to point out uncertainties.
Even if Bibi Le is not the expert its commentaries are very usefull. A topographical analysis of the Type Strain (or types strains) position (within the tree or outside) is done : Bibi Le evaluate the node distance between the query and all the strains known in the Type Strains Data Base within the tree, in the Data Base, and points out missing Type Strains in the tree.
In some cases species type strains sequences sharing the same node upward are not found in the tree, this may be due to the position of the primers (another part of the gene was studied) or to identification errors :

You can have a look at the sequences by clicking on the Gen Bank Id.
In other cases a Type Strain sequence may have been introduced in the alignment, but is rather far from the best matching sequences. In this case a button appears and clicking it forces inclusion of the missing sequence (or missing sequences) in the tree.

Note that in the figure above, both button and missing type strains indication is given.
Other commentaries are possible, like the :

warning for a lack of biodiversity (flat tree, one species).

Phylogenetic Tree

This is the most important information given by Bibi Le !
Learn how Bibile is Calculating Tree.

You can see the phylogenetic relations between all the strains and additionnaly click on the links...
Note: the default number of incorporated sequences is 30, better job is often done with 50-75 sequences.

Reading Codes

• Sequences identities with the query are indicated by the color of the symbol :

• The (very) small number at the end of the line indicates the first, second, third positions in a BLAST score.

• A Type Strain is indicated by :

• A Type Strain whose name is not already in the Nomenclature Data Base appears like this :
  
• A sequence obtained from complete genome data belongs of course to a well known strain with correct identification ; it appears like this :
  

  Note that if the strain has the TS status, C is not shown.

• A "non Type Strain" (an isolate without this quality) is identified by a small i after the name :

• But if the name has no standing in nomenclature, a ? appears :

See how a bad description in Gen Bank led to a bad recognition by Bibi Le in the last case.

• The X indicates that the phylogenetic position of the strain is known to be unrelated to that of the species, the identification given to the strain in Gen Bank is dubious (this is not due to Gen Bank, but to identification errors, contamination, etc.). For Bibi Le, the strain sequence is blacklisted :

• A variant (biovar, serovar, pathovar) is indicated at the end of the line :

• But the Ly indication like here signify that the sequence was done by our team.:

• The specific host, if indicated in Gen Bank features is indicated like this :

Thus the "<" indicates the origin

but sometime the bacteria is an endosymbiont, this relation to the host is symbolized like here :

The host name appears between <{host_name}

The endosymbiotic nature of the bacteria may be given without an extractable name of host like from Gen Bank features :

This is the case of an endosymbiont not identidied by the algorithm we use in the program : the host name is only given, without {}

In some cases the host feature is very large :

Links

A link is indicated on the species name, this is a link to DSMZ [1], another link is mentioned on the Gen Bank Id, this is a link to PBIL and Gen Bank data.

Buttons

The buttons line looks like :

Alignment Cleaner

During alignment some "trailing" nucleotides may appear, both in the query line or in the others. The Aligment cleaner suppress these erroneous nucleotides, as well as the excess of "N" positions at the both end of the sequence. In some cases, improvement of the identification is obvious, see the sample sequences in the SSU-rDNA-16S_stringent test-set to test it.

Tree scale

This button and options menu enables to reduces the scale of the tree.

Alignment viewer

You can see the alignment using Sequence_Colourist [2]
either to see the whole alignment or only the section corresponding to your query. This html viewer is very easy to use but for very broad and/or long aligments, you may have to wait a while.

Printing

Printing of a very simple and badly configured report is possible by using

As concern the tree, a PDF file can be used and printed :

You have to choose dimentions for printing and police :

The pdf picture file is generated and then you can print by clicking on the link :

Raw files

• The FILES for further work by your own
  • To get the .ph files (tree) or alignment (alnfinal.aln) etc.
  • Many are not of any use outside for developpers.
• The BLAST suggestions (an html file)

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