BLAST - Setup: Configure BLAST job parameters

[NShaforostov]

The BLAST panel from which the BLAST search will be performed shall have conventionally the following view, e.g.:

The BLAST panel should contain two sub-tabs:

• Search - to display and specify search settings, and also start a new search
• History - to display the history of searches

Search settings

In the Search sub-tab, the following elements should be:

• selector of the TOOL that will be used for the search (mandatory). Only one tool shall be selected at a moment:
  • blastn - for the search over nucleotide databases using a nucleotide query
  • blastp - for the search over protein databases using a protein query
  • blastx - for the search over protein databases using a translated nucleotide query
  • tblastn - for the search over translated nucleotide databases using a protein query
  • tblastx - for the search over translated nucleotide databases using a translated nucleotide query
• the QUERY SEQUENCE (mandatory section). This section shall contain:
  • text field for a sequence specifying
  • checkbox and control to select a sequence file from the local workstation
  • only one entity - text field or sequence file - should be used for the search. By default the sequence from the text field will be used. To use a file with sequence instead text field, user shall:
  • tick the corresponding checkbox (see mockup) - in this case, text field for a query should become disabled
  • click the "Choose file" button and select the file with a sequence from the local workstation
  • for an upload file, the file name should be appear near the "Choose file" button
  • for selection another file if needs, click the "Choose file" button again and repeat steps as above
  • the common flow of the search sequence definition should be used:
  • if the "upload" checkbox is disabled and the text field contains the sequence - this sequence shall be used for a search
  • if the "upload" checkbox is disabled and the text field is empty - the search shall not be performed
  • if the "upload" checkbox is enabled and the sequence file is chosen - this sequence file shall be used for a search
  • if the "upload" checkbox is enabled and no sequence file is chosen - the search shall not be performed
• text field for the search task title (optional field). In this field, user may specify the title for the current search operation - to easier find it later, e.g.:
• search "set" (mandatory section). Here user can specify where the search should be performed:
  • DATABASE dropdown list - for the select of the BLAST database (mandatory), e.g.: Displayed list of databases should correspond one of the types - protein or nucleotide. This type is defined by the selected tool type at the TOOL selector: for blastn, tblastn, tblastx - nucleotide databases should be displayed, for blastp, blastx - protein databases should be displayed. If no database is selected, the search shall not be performed
  • ORGANISM dropdown list - for the select/specifying the species for which the search should be performed (optional)
  • each organism should be displayed in format: <name> (taxid: <taxonomyID>), where <name> - organism name, <taxonomyID> - taxonomy ID of that organism
  • checkbox to exclude the certain organism(s) from the list for which the search should be performed (unchecked by default)
  • this dropdown list shall support multi-select. If there are several species selected in the dropdown list and the Exclude checkbox is set - all selected organisms shall be excluded from the search
• ALGORITHM dropdown list (mandatory) - list of algorithms available for the current tool:
  • for the blastn tool, there should be:
  • megablast (highly similar sequences) - default value
  • discontiguous megablast (more dissimilar sequences)
  • blastn (somewhat similar sequences)
  • blastn-short (optimized for sequences less than 30 nucleotides)
  • for the blastp tool, there should be:
  • blastp (protein-protein BLAST) - default value
  • blastp-short (optimized for query sequences shorter than 30 residues)
  • blastp-fast (faster version that uses a larger word-size)
  • for the blastx tool, there should be:
  • blastx (search proteins using a translated nucleotide query) - default value
  • blastx-fast (faster version that uses a larger word-size)
  • for the tblastn tool, there should be:
  • tblastn (search translated nucleotide databases using a protein query) - default value
  • tblastn-fast (faster version that uses a larger word-size)
  • for the tblastx tool, this dropdown list should be unavailable (invisible)
• "Additional parameters" section - collapsible section to specify additional "technical" BLAST parameters that should be used for the search. Expanded view of that section, e.g.: Where:
  • Max target sequences (integer, greater than 0) field allows to set the maximum number of aligned sequences to display in results (CLI BLAST option max_target_seqs)
  • Expect threshold (real, greater than 0) field allows to set expect value for saving hits (CLI BLAST option evalue)
  • Options field allows to specify additional blast options in CLI style. If user will try to specify such options in incorrect format or with incorrect names - they should be ignored during the search. Near that field, the "Info" button should be placed - by click this button the help info/page with all possible CLI options shall appear (see details below, in comment)
  • Max target sequences and Expect threshold settings should have default values. These values shall be defined in System settings that stored on the server side and could be changed only by system administrator. System administrator shall have the ability to change values of these settings "on-the-fly", without app redeployment. So, if user doesn't forcibly specify values for these parameters (e.g., even doesn't expand the "Additional parameters" section) - their default values shall be used for the search. As "base" default values, I suggest: Max target sequences - 250, Expect threshold - 0.001
• Search button - to start a search

[NShaforostov]

Bug was found:

blastn tool type should be selected by default when BLAST tab is opened from "Views" menu or a read at track. Currently, there are cases when no tools are selected, e.g.:

Fixed.

[NShaforostov]

Addition:

There should be "Clear selection" buttons at "Organism" dropdown list and "Query sequence" field - to clear the corresponding input. E.g.:

[NShaforostov]

Addition:

There should be support for specifying the "Expect threshold" value in scientific notation, e.g.:

[NShaforostov]

Minor addition:

Change the label near the "Organisms" dropdown list to "Exclude" (instead of "Excluded")

[NShaforostov]

Bug was found:

In the "Organisms" dropdown list, an empty place appears when several items have already selected, e.g.:

Verified

[NShaforostov]

Addition:

I suggest to hide a placeholder for the "Organisms" dropdown list when any item have already selected, i.e.:

[mzueva]

Database list shall be filtered according to selected tool:

• blastn, tblastn, tblastx - nucleotide databases should be displayed
• blastp, blastx - protein databases should be displayed

[NShaforostov]

Addition:

User shall have the ability to view "help" info about possible options that he(she) can specify to the "Options" field in the "Additional parameters" section. For that:

• near the "Options" field, the "Info" button should be placed, e.g.:
• on-click that button, a new tab with "help" page shall be opened:
  • "help" page - it is one of the static html pages with a name according to the tool type (blastn.html, blastp.html, blastx.html, tblastn.html, tblastx.html) that will be placed at path server/catgenome/src/main/resources/static/
  • "help" page should be opened according to the tool selected at the tool selector
• the "Info" button shall have the tooltip Show possible options help

[NShaforostov]

Addition:

User shall have the ability to view "help" info about possible algorithms that he(she) can select in the "Algorithm" dropdown list. For that:

• near the "Algorithm" dropdown, the "Info" button should be placed, e.g.:
• on-click this button, the tooltip shall appear with short description of available algorithms for the selected tool type

I suggest the following tooltips:

• for the blastn tool:

  Four different algorithms are supported:

  • megablast - for very similar sequences (e.g., sequencing errors)
  • discontiguous megablast - for more dissimilar sequences, typically used for inter-species comparisons
  • blastn - the traditional program used for inter-species comparisons
  • blastn-short - optimized for sequences less than 30 nucleotides

• for the blastp tool:

  Three different algorithms are supported:

  • blastp - for standard protein-protein comparisons
  • blastp-short - optimized for query sequences shorter than 30 residues
  • blastp-fast - a faster version that uses a larger word-size

• for the blastx tool:

  Two different algorithms are supported:

  • blastx - for standard translated nucleotide-protein comparison
  • blastx-fast - a faster version that uses a larger word-size

• for the tblastn tool:

  Two different algorithms are supported:

  • tblastn - for a standard protein-translated nucleotide comparison
  • tblastn-fast - for a faster version with a larger word-size

[maryvictol]

Attempt to start Search with algorithms discontiguous megablast and blastn-short selected for blastn tool gives errors "discontiguous megablast" is not correct algorithm for "blastn" and "blastn-short" is not correct algorithm for "blastn" correspondingly.

Fixed

[maryvictol]

Search tab with empty fields, without any selected Tool and with empty error message opens at return to the Search tab from History tab after any search. Steps to reproduce:

1. Configure Search parameters and click Search button >> History sub-tab opens automatically
2. Open Search sub-tab

Verified as fixed

[maryvictol]

Exclude button is displaced out of the screen at case of long Organism name.

[maryvictol]

Exclude button is displaced out of the screen at case of long Organism name.

Verified as fixed

[maryvictol]

Bug was found: @rodichenko. Error messages don't disappear after removing the cause and can't be closed.

Verified as fixed

[Tatyana2022]

Bug was found: Organism field has case-sensetive highlight of search results All matching results should be highlighted, regardless of case @DmitriiKrasnov

Verified

[Tatyana2022]

Verified

[NShaforostov]

Docs were added via #566 and located here.