The Desktop Application

This section describes briefly the main parts of the Blast2GO applications.

Main User Interface

The general components of the Blast2GO main user interface are:

1. Menu Bar: The main application menu contains 5 items:
   • File: This menu groups all functions for opening, saving and closing Blast2GO files as well as to load or export data in many different formats.

   • Analysis: This menu hosts different options for the analysis of your datasets like e.g. computing GoSlim view, Enzyme Code annotation and performing statistical analysis of GO distributions for groups of sequences.

   • Tools: This menu contains rather technical features for data-manipulations like batch-renaming, ID mapping, data redundancy checks etc.
   • View: This menu allows to open different utility taps like the file manager, the application messages or the Java memory monitor.
   • Help: The help menu provides access to various support features. You can review your subscription details, the CloudBlast history and the App-Manager. The App-Manager allows to install and update additional tools for Blast2GO.

   
   

2. Main Analysis Icons: These will execute the whole analysis.
   • start: Quick start to load a Blast2GO Project or recent projects or fasta sequences or annotation file.
   • genefind: Allows to run eukaryotic and prokaryotic gene predictions.
   • blast: Contains functions for performing BLAST searches and resetting results.
   • interpro: It will run the InterProScan, reset the results or merge the GO results to the existing Annotation.
   • mapping: This function fetches GO terms associated to hit sequences obtained by BLAST.
   • annot: Includes different functions to obtain and modulate GO
   • charts: The Charts icons collects a number of chats that are generated during the BLAST, mapping and annotation processes. They are aimed to offer the researcher an overview of the results obtained in each step to facilitate the decision for parameter choice in latter annotation steps.
   • graphs: Allows to make Combined and Colored Graphs as well as Single Graphs by providing GO IDs or GO Terms.
   • select: Allows to make sequence selections based on the sequences status (colors), names, GO terms and descriptions as well as delete selected sequences from a project.
   • diff-expr: Allows to perform pairwise and time-course expression analysis for un-normalized read counts.

   
   

3. Application Tabs:
   • Progress tab: Shows running, queued and finished jobs. Allows to stop jobs and open a separate log-viewer. Each finished job shows the time it took to execute. A finished job can be removed using the cross button. All finished jobs can be removed by clicking on the small triangle in the top left corner.
   • Application Messages tab: Displays information on the progress of the analysis.
   • File Manager: The File Manager allows to view, open and organize different Blast2GO related files.
   • Java Memory Monitor: Provides information about the memory consumption of the application.
   • Log tabs: Most of the analysis steps provide additional logging. These logs can be viewed via the Progress tab.

   
   

4. Data Tabs: Each object type can be opened and saved in a separate tab. In general, table viewer tabs like e.g. the Blast2GO sequence table will be opened by default in the upper-wide area while result tabs will be opened in the lower-right area (e.g. charts, graphs, etc.).

The Blast2GO File Manager allows to view, organise and open different Blast2GO related files.
The "Merge'' option allows combining various file into one. The merge function may not be available for all data types and can only be used to object of the same type.

The Table

The table allows to open different types of objects (.b2g files) in spreadsheet style. Additionally to the columns representing the dataset it contains a TAG column which represents the different status of each line according to the object type. 
The table allows to hide or show single columns via a checkbox menu by right-clicking on the column header. In case, multiple objects are viewed (e.g. Blast2GO plus Rfam results), column headers are colored differently. In this example (Figure 4) tags show if a functionally enriched GO term is over or under represented.

Table Context Menu

The context menu allows to create ID lists of a selected column, extract subsets of entries as well as to copy part of the content into the clipboard. The values of a given column can also be visualized as a category or distribution plot in various formats (bar-chart, pie-chart, etc.).

• 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.
• Copy Sequence Names to Clipboard: Copies the sequence name to the clipboard.
• Change Annotation and Description: Allows to manually change/add annotations.

• Annotate Sequence: This function allows changing annotation parameters for the selected sequence and re-running automatic annotation.

• Make Graph of GO-Mapping-Results with Annotations Score: Displays a DAG with all GO terms related to one sequence. Shows all the GOs from the mapping step as well as final annotations (highlighted).
• 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 (see Figure 6).
• 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.

Create ID lists:

To generate an ID list the desired sequences have to be marked and then right click on "Create ID list from selected Entries (SeqName column)''.
A new tab is opened containing the ID list of the marked sequence names. This list can now be saved for further use (e.g. enrichment analysis, selections, etc.). It is also possible to generate sequence ID lists from Graphs (10.1).

To mark all the sequences on the table do: Ctrl + A (Windows/ Linux) and Apple + A (Mac).

The ID lists can be used in:

• Fisher Exact Test
• Select Sequences
• Load Annotations from BioMart (online)

The Gene Set Enrichment Analysis (GSEA) needs a ranked list and this can also be generated by Blast2GO with the Create ID Value List.

Here is an example of the Open File dialog of the Fisher's Exact Test Wizard shows the available ID lists if the selected file type in the checkbox (bottom left) is set to B2G ID list.

Filter out Sequences

The Blast2GO table allows to filter out rows, depending on different search criteria for each column. Each column header shows 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.
• On the top-right corner there is a small status message showing how many sequences pass your filter.
• The button next to it (crossed out document) removes all current filters.

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.