BLAST Results - View job details: View sequence details - alignments

[NShaforostov]

User shall have the ability to view details about all matches (alignments) of the search query to the certain sequence from the BLAST search results.

For that, user should click the certain row (sequence) in the sequence table (#430). The form with details about all matches (alignments) of the search query to the certain sequence shall be opened. "Alignments" form should be opened in the same tab ("History"), e.g.:

This form shall contain:

• Back button - to hide "Alignments" form and return to the sequences table view (#429)
• Sequence ID and its Definition (if it's specified for the sequence). ID should be a hyperlink:
  • if the search was performed on the NCBI database - this hyperlink shall open a corresponding sequence page on NCBI
  • if the search was performed on the "custom" database - this hyperlink shall open a corresponding reference and its chromosome (to which this sequence belongs) in the "Browser" panel
  • type of the database should be defined by specific flag during the database upload into NGB
• Details about all matches of the search query to the current sequence (match blocks)

Each match block should contain:

• range (positions) of the current sequence where the match is defined
• "View at track" link - hyperlink to view the certain match (alignment) to the current sequence (see details in #433). This hyperlink shall be visible only for those sequences which reference files are in NGB databases
• score and bit-score
• expect value (E-value)
• count of identities between sequences (by symbols) and its percent value
• count of gaps (by symbols) and its percent value
• block with the conventional figure of the query string alignment to the current sequence segment:
  • start and end position of the query string segment
  • aligned query string segment
  • start and end position of the current sequence segment
  • the current sequence segment to which the query string segment was aligned
  • only for nucleotide sequences: strands of each sequence (query and subject) - plus or minus
  • symbols that "link" the corresponding letters in both sequences:
  • straight line if letters are equal
  • nothing (empty) if letters are not equal (mismatch)
  • minus symbol ("-") in any sequence - for gaps Example:
• if aligned part of the query sequence/subject sequence is longer than width of the shown BLAST panel, both sequences shall be split on parts (up to panel width) and placed one above the other, e.g.:

[NShaforostov]

Addition: Format of the "score" field should be:

Score: <bitscore> bits (<score>)

Where <bitscore> - value of an alignment score in bits, <score> - value of an alignment raw-score

Currently, we display alignment length value in parentheses.

[Tatyana2022]

Addition: Format of the "score" field should be:

Score: <bitscore> bits (<score>)

Where <bitscore> - value of an alignment score in bits, <score> - value of an alignment raw-score

Currently, we display alignment length value in parentheses.

Fixed

[Tatyana2022]

Bug was found

Missing Organism value in parentheses for Sequence Id field

Currently, N/A value displays

@DmitriiKrasnov

Fixed

[Tatyana2022]

Sequence ID is not a hyperlink if search was performed on the custom database as described above. Should it be a hyperlink? If so, should it display all sequences on track or is it enough o have View at track button for each sequence? We haven't found an exact answer. Maybe something was decided earlier? Could you take a look at it, please? @mzueva

[rodichenko]

Sequence ID is not a hyperlink if search was performed on the custom database as described above. Should it be a hyperlink? If so, should it display all sequences on track or is it enough o have View at track button for each sequence? We haven't found an exact answer. Maybe something was decided earlier? Could you take a look at it, please? @mzueva

if the search was performed on the "custom" database - this hyperlink shall open a corresponding reference and its chromosome (to which this sequence belongs) in the "Browser" panel

@mzueva @Tatyana2022 1e5cbf5b7f01d128d7422d5df6d1112cd95948ba implements navigation to the chromosome.

Fixed

[Tatyana2022]

Bug was found It is impossible to reopen reference and its chromosome (to which sequence belongs) in the "Browser" panel after clicking on View at track button

Steps:

1. Go to the BLAST
2. Open 388 Task Id in the Search History
3. Click on 13 sequence in the Sequence results table
4. Click on 13 Sequence ID
5. Click on View at track button of any alignment
6. Click again 13 Sequence ID

Expected result: @DmitriiKrasnov @mzueva

Fixed

[Tatyana2022]

Bug was found Sequence ID link with a long name isn't open a corresponding reference and its chromosome (to which this sequence belongs) in the "Browser" panel (E.g. Sequence ID = gb|GL000213.1 in 388 Test ID) @AlfiyaRF @mzueva

Fixed

[Tatyana2022]

Bug was found No View at track button for Sequence with long ID (E.g. Sequence ID = gb|GL000213.1 in 388 Test ID)(Custom database) @DmitriiKrasnov @mzueva

Fixed

[Tatyana2022]

Verified

[NShaforostov]

Docs were added via #566 and located here.