BLAST Results - View job details: Navigate to the genomic location within the NGB

[NShaforostov]

User should have the ability to view any found match (alignment) at a track (graphic visualization) in the "Browser" panel. To open the visualization form, user should click the "View at track" link near the match in the "Alignments" form (#432).

An alignment of the nucleotide sequence, opened by such a hyperlink, should look something like:

Example above is shown for the following match block:

The workflow should be the following - user clicks the hyperlink "View at track" and:

• if the current opened reference/chromosome in the Browser panel is distinct from the reference/chromosome to which the sequence from the BLAST results belongs:
  • current opened reference/chromosome and all related tracks shall be closed
  • in the Browser panel, the reference/chromosome to which the sequence from the BLAST results belongs shall be opened:
  • if for that reference, there are gene annotation files in NGB, their tracks shall be automatically opened too
  • in the Browser panel, additional track for the search query shall appear
• if the current opened reference and chromosome in the Browser panel are the same reference and chromosome to which the sequence from the BLAST results belongs:
  • in the Browser panel, only additional track for the search query shall appear
• if user will click the hyperlink "View at track" for another alignment but on the same reference that is already opened - another one additional track for the search query alignment should be opened (i.e. separate track for each clicked aligned range of the same subject reference)
• all other behavior of the Browser panel should stay as currently implemented

So, already opened additional tracks for the search query alignments will be automatically closed in any of these cases:

• user clicks the hyperlink "View at track" for an alignment related to a reference distinct from the currently opened
• user selects another chromosome for displaying in the Browser panel
• user selects in the "Datasets" panel a dataset with a reference distinct from the currently opened

Details of the visualization:

• at the reference track, by default, the strand according to the strand of the subject sequence of the certain alignment should be selected
• for the search query - track that shows alignment of the search query to the sequence:
  • on a track, only search query shall be shown
  • track shall be displayed in the similar manner as a single read at the ALIGNMENT track in the "Browser", in which:
  • query matches - should be shown as a gray line by width of aligned matches -
  • query strand - should be shown as an arrow on the edge of the query line -
  • mismatches - should be shown as separate color rectangles with the corresponding letters -
  • gaps in sequence - should be shown as insertions (a perpendicular violet line in the gap position) -
  • gaps in query - should be shown as deletions (a black line linked two "separate" parts of the query) -
  • additionally, near the each end of the query line at the track, should be conventionally shown counts of the query positions that were not aligned to sequence - . For example above, first 3 symbols and last 2 symbols of the query were not aligned
• user shall have the ability to move query track among other tracks
• by default, the reference scale shall be set to show the full query line in maximum possible zoom

An alignment of the protein sequence, opened by such a hyperlink, should look something like:

Additional details of the visualization of alignments from BLAST Search results over protein sequences:

• at the reference track, by default, the translation lines should be enabled
• at the "Browser" panel, the target genome shall be loaded at the coordinates of the gene to which the subject sequence belongs
• for the search query:
  • a separate track that shows subject sequence conventionally as a whole gene to which it belongs. Should be shown as long rectangle
  • if there are more matches - they all shall be displayed in the same manner at this track
  • above each sequence its ID should be displayed

[NShaforostov]

Addition:

Add displaying of an info tooltip when hovering over the nucleotide sequence alignment on the track. Such tooltip shall contain the following info about the certain alignment:

• score and bit-score
• expect value (E-value)
• count of identities between sequences (by symbols) and its percent value
• coverage percent value of a query sequence
• count of gaps (by symbols) and its percent value
• count of mismatches (by symbols)
• count of unaligned symbols in a query sequence

For example:

[Tatyana2022]

Verified

[NShaforostov]

Docs were added via #566 and located here.