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Variant search

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Anna Bernasconi edited this page Sep 23, 2020 · 17 revisions

The Variant search section, just below the Metadata search section, allows searching sequences based on the variants they have with respect to the reference nucleotide sequence, the impacts of such variants (as an annotation obtained from SnpEff), and the amino acid changes with respect to reference protein sequences.

As a first choice, the user should select between:

  • Add condition on amino acids
  • Add condition on nucleotides

variant-search

In both scenarios, the user is provided with a series of drop-down menus to refine her search.

Amino Acid Variant-search

aminoacid-query

Nucleotide Variant-search

nucleotide-query

Query composition

When the user selects or a dedicated mask is opened, with a series of dropdown menus for filters selection (click on the to read the filter definition).

Each search session can be submitted by pressing . In case the choice needs to be reset, the user can press .

Note that, when a variant search is running with a specific string, until either the or the button is clicked, all other search options are disabled (specifically the upper Metadata search part). This is necessary to prevent inconsistencies in the shown results.

Once the choice is accepted, it is registered as a Nucleotide/Aminoacid query panel, which memorizes the information of the search. A previously applied search can later be dismissed by pressing the button.

A user can also add multiple search sessions (of the same kind, either amino acid or nucleotide) before pressing . To add another search query it is necessary to press , which registers the previous search and provides a new empty mask to insert a new search. This is added in 'disjunction' (i.e., alternative) to the previous one.

aminoacid_query_combination

Note that, when is pressed, the multiple variants selected in one Nucleotide/Aminoacid query panel are intended as alternative.

Once the result is saved (as described in the 'Aminoacid query' or 'Nucleotide query'), the user can open a new search session by pressing again or . At this point, variants selected in different search sessions, are instead intended as coexisting conditions in the resulting item set. Note that amino acid variant searches and nucleotide variant searches can only be combined in different search sessions (therefore combined in disjunction).

aminoacid_nucleotide_combination

In the shown example, the user is choosing all items that have:

(

Amino acid query: (gene_name = 'E', sequence_original = 'A', sequence_alternative = 'G')

OR

Amino acid query: (gene_name = 'E', sequence_original = 'A', sequence_alternative = 'H')

)

AND

Nucleotide query: (gene_name = 'E', sequence_original = 'C', sequence_alternative = 'T')

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