MicroScope - Tutorial
What is the aim of the Comparative Analysis tool ?
To find a set of mutations present in some organisms and absent from others.
How to use this tool ?
- Choose one or several reference sequences.
- Select at least one clone or lineage in which you’d like to find mutational events, and optionally one or several clones/lineages from which the selected mutations are absent.
- If you want, you can play with:
- the nature of the relevant mutations,
- their location on the reference genome,
- 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.
- Finally, choose the additional characteristics you want to appear in the table of results, knowing that the nucleotide changes are displayed by default.
- And submit your query.
Trick : The content of the two main selection lists can be customized thanks to the links of the "Focus on" sub-section.
Trick : The "ALL selected clones/lineages" option allows to select only mutational events that are present in EVERY SELECTED clones or in EVERY CLONES of the selected lineage(s).
How to read the table of results ?
You have one table of results for each reference sequence selected. Each result table is composed of 2 main parts : A and B.
A. In the left part of the table, mutations are localized on the reference sequence and replaced in a genomic and functional context:
- Abs(olute) Position: Position on the reference sequence.
- Rel(ative) Position: Position on the Genomic Object affected according to the first base of the latter, for genic events only .
- 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.
B. In the right part of the table, mutations are described according to the displayed characteristics chosen by you and allocated to the clones they belong to.
- Whatever the displayed characteristics chosen, you will have access to a full mutation description if you mouseover a mutation:
Mutation type | [SNP type] | Nuc. change | [Nuc. change effect] | [Codon change] | [AA change] | [AA change effect] | Numerical score | Fractional score | Sequencing technology | Read type | Source
Fields in brackets are specified for SNP events only.
- Mutation type: ’SNP’, ’insertion’ or ’deletion’.
- SNP type: ’hom’ (homozygous), ’hez’ (heterozygous), ’xyx’ (the variant of heterozygous SNPs like X -> Y/X).
- Nuc(leotide) change: ref_base/new_base.
- Nuc(leotide) change effect: ’ts’ (transition) or ’tv’ (transversion).
- Codon change: ref_codon/new_codon.
- AA change: ref_AA pos_AA new_AA.
- AA change effect: ’syn’ (synonymous), ’missense’ or ’nonsense’.
- Numerical score.
- Fractional score: local_coverage/total_coverage.
- Sequencing technology: ’solexa’ or ’454’.
- Read type: ’se’ (single-end) or ’pe’ (paired-end).
- Source: ’automatic’ (SNiPer’s prediction) or ’validated’ (experimental validation).
- If you look carefully, evolved clones are grouped by lineage and ordered according to their timepoint in each lineage. As a consequence, the dynamics of genomic changes can easily be drawn during the studied evolutionary time.
Trick: You can export the Genomic Objects reported in the result table to a private Gene Cart thanks to the "Export to Gene Cart" button.
Is it possible to have a synthetic view of the results ?
Yes, of course! Below the table of results, you have another section, called "Summary" which lists and classifies all the mutational events reported for each selected clones.