MicroScope - Tutorial   »   Variant Discovery   »   Evolution Projects   »   Parallelism Analysis


What is the aim of the Parallelism Analysis tool ?

To identify genetic variations OR mutated Genomic Objects (GO) SHARED BY several clones in different lineages.

How to use this tool ?

First of all, choose the subject of your analysis ("Shared Mutations" or "Shared Mutated GOs") in the "Focus on" sub-section.

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The "Shared Mutations" mode:

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The "Shared Mutated GOs" mode:

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Then, the procedure is quite similar in the two analysis modes:

  1. Select a reference sequence.
  2. Specify:
    • the way you define identical mutations, knowing that, by default, they must have the same position on the reference sequence (in the "Shared Mutations" mode only).
    • the numbers of lineages and clones in which you’d like to retrieve the same mutations or mutated GOs.
    • the standpoint of your analysis: inclusion of all the evolved clones or selection of clones sampled at a specific timepoint.
  3. If you want, you can play with:
    • the nature of the relevant mutations,
    • their location on the reference genome (in the "Shared Mutations" mode only),
    • the sequencing technology used to produce the data from which the mutations have been predicted,
    • the mutation score,
    • the portion of the reference sequence which must be screened, and
    • the length of the mutations.
  4. Submit your query.

How to read the table of results ?

A. In the "Shared Mutations" mode:

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1) Description of common mutations: It depends on your definition criteria.

2) Genomic context:

  • Rel(ative) Position: Position on the Genomic Object affected according to the first base of the latter, for genic events only [1].
  • GO Label: Each label encompasses a link to the information form of the Genomic Object considered.
  • GO Description: [GO_gene_name] | GO_product | GO_begin | GO_end | GO_frame
    • Genic events: description of the Genomic Object affected
    • Intergenic events: description of the flanking Genomic Objects, i.e. the nearest upstream (blue) and the nearest downstream (purple) GOs.
  • Distance to the flanking GO: Distance between the intergenic events and the end of their nearest upstream gene (blue) or the begin of their nearest downstream gene (purple), whatever the reading frame of the laters.

3) Distribution of the clones sharing the same mutations according to the lineage they belong to:

  • Lin Nb: Number of lineages where the same mutations are detected.
  • EO Nb: Number of evolved organisms sharing the same mutations.

Be careful: The result number may change depending on how identical mutations are defined!

B. In the "Shared Mutated GOs" mode:

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1) Description of common mutated GOs:

  • MoveTo: Click on the icon glass to access to the genomic map of the reference sequence centered around the mutated GO.
  • GO Label: Each label encompasses a link to the information form of the Genomic Object considered.
  • GO Type: ’CDS’, ’fCDS’, ’rRNA’, ’tRNA’ or ’misc_RNA’.
  • GO Description: [GO_gene_name] | GO_product | GO_begin | GO_end | GO_frame

2) Distribution of the clones sharing the same mutated GOs according to the lineage they belong to:

  • Lin Nb: Number of lineages where the same mutated GOs are detected.
  • EO Nb: Number of evolved organisms sharing the same mutated GOs.

Trick: In both cases, you can export the Genomic Objects reported in the result table to a private Gene Cart thanks to the "Export to Gene Cart" button.