User Interface

Blast2GO functions are seamlessly integrated within the workbench. All mayor functions can be accessed via the Blast2GO section in the Toolbox.

Content of this page:

Sequence Table

The sequence table is the main view of a Blast2GO Project, where each row represents a sequence. Colors indicate the status of each sequence, starting from white (without analysis results), to orange, green, blue, etc. (see figure below). The sequence table also offers a context menu with several additional options for each individual sequence, like (blast result details, sequence information, manual annotation modifications, etc.).

Image colours

Figure 1: Different color codes indicating the status of the sequences

Sequence Table Context Menu

  • Show Sequence: Allows to see the sequence information.
  • Show Blast Result: Revise the Blast results in detail:, hits, species, identifiers, etc.
  • Show InterProScan Result: Revise the InterProScan results in detail: databases, GOs, etc.
  • Show Mapping Result: Revise the retrieved candidate GO terms in detail: Accessions, Evidence Codes, Databases.
  • Show GO Description: Review information about annotated GOs.
  • Change Annotation and Description: Allows to manually change/add annotations.
  • Extract Selection to new Tab: Create a new project from the marked sequences (Shift or Ctrl).
  • Copy Selection to Clipboard (tabular format): Copies the marked sequence to the clipboard in tabular format for further processing in a spreadsheet editor.
  • Copy Content of Column: SeqName to Clipboard: The content of a specific column will be copied to the clipboard.
  • Create ID List of Column: Sequence: Allows to create an ID list of a specific column which can then be used for Fisher's Exact Test or Selection of sequences.
  • Create ID Value-List of SeqName and Length: Allows to create a list with two specific columns e.g. SeqName and Length.
  • Create Category Chart of Column: Length: Create a category chart of a certain column e.g. sequence length.
  • Create Distribution Chart of Column: InterProScan IDs: Create a distribution chart of a certain column.

Filter out Sequences

The Blast2GO table allows to filter out rows, depending on different search criteria for each column. Each column header show a small icon which opens a context menu when left-clicked.

  • Filters can be applied in various columns and are joined via an AND condition.
  • Different data-types allow different filter settings (e.g. numbers allow greater than).
  • When a filter is applied on a column the filter icon turns red - double clicking the icon will remove the filter.
  • The side panel on the right-hand side shows how many rows are currently visible.
  • The button below it, Clear Filters, removes all current filters and show all rows.

All the algorithms, blast, mapping, annotation, etc., work on the selected sequences and not only on the filtered ones. This means if one has a filter but there are some sequences selected on your project and one runs e.g. remove blast results, it will work on all selected sequences and not only on the ones you see on the table.

Hide Columns

This feature allows to hide the columns of the sequence table.
By right clicking on a column and a menu will be displayed and one can select those columns to hide from the table. In combination with Export Table from the side panel, this can be used to customize the output.

Figure 2: Sequence Context Menu

Figure 3: Filter Criteria

Figure 4: Hide Columns

Side Panel

The Sequence table offers a side panel which allows to select, filter and search sequences within a Blast2GO project.Filter: Blast2GO table allows to filter sequence out. Here one can see the number of sequences that are on the table and also to reset the filter options.

  • Selection: Allows to select, deselect, invert, delete and extract a given selection.
  • Select by State: Allows to make a selection based on the sequence status (colors).
  • Select by: Allows to select sequences based on their name, description, species, function (GO terms or IDs), description, gene name, enzyme code or InterPro ID. The selection-type, exact search (whole word (important for IDs) has to match) and case sensitivity can be chosen. A search criteria can be provided via a search field. Alternatively a list of sequence names or GO functions can be loaded via a text file or an ID List. The 3 buttons let you choose between starting a new selection, adding rows to the current selection and removing rows from the current selection.

Figure 5: Side-Panel