Dinucleotide Properties Genome Browser

2 Interface

2.1 Main window

The DiProGB main window contains the following elements:

Title bar

Shows the DiProGB version.
Graphics controls

Menu for controlling the shifting window size, the y-axis graph scaling and the type of the mouse wheel action (y-axis graph scaling, shifting window size, sequence zoom).
Strand controls

Menu for strand selection.
Statistics

Menu for generating a statistics table, different corresponding random graphs, the mean value of the displayed region (observed), and the expected mean value (arithmetic mean of the 16 dinucleotide values).
Right title bar buttons

Minimize, maximize the DiProGB window or close the program.
Main menu

The main menu offers basic functionalities such as to open, save or print data, motif and repeat search as well as Fourier transform options, editors for GenBank files and for dinucleotide properties, graph display options and help file access.
List menu

The list menu comprises buttons for controlling the following lists: selected sequences, available dinucleotide properties, features and qualifiers, and position info for ‘walking‘ with the mouse cursor through the sequence.
Vertical scrollbar

Moves the whole graph along the y-axis (vertically).
Horizontal shift buttons

Moves the graph to the left or right (on the x-axis) as long as the begin or end of the sequence is not reached.
Left sequence position

Specifies the leftmost sequence position displayed in the DiProGB window. The min button sets this value to the first nucleotide of the sequence and the go button applies the changed position and redraws the graph.
Middle sequence position

Specifies the middle position of the sequence range shown. Entering a different value shifts the whole sequence to the left or right accordingly. The go button applies the changed position and redraws the graph.
Right sequence position

Specifies the rightmost sequence position. The max button sets this value to the last nucleotide of the sequence (its length) and the go button applies the changed position and redraws the graph.
Status line

This line contains information about the displayed genome, the selected dinucleotide property, the number of its features and qualifiers or the status of running processes.
Horizontal scrollbar

This blue scrollbar indicates the selected sequence range of the sequence graph. By default the complete sequence is selected which means that the blue bar extends from the leftmost to the rightmost position of the main window. If only a part of the complete sequence is displayed, the bar indicates the location of the selected range in the genome. The fixed sequence interval can also be moved through the complete genome.
Popup menu

Pressing the right mouse button in the DiProGB main window activates the following popup menu (given a sequence has been loaded before).

This menu is for quick changing different mouse wheel fuctions and for accessing the nucleotide sequence and its features.

Zoom

After zooming at least once into the sequence graph the arrow buttons are activated and can be used to switch between the previously selected parts of the sequence.
Mouse wheel

The user can choose amongst three functions for using the mouse wheel: y-scaling = changing the amplitude, SW size = changing the shifting window size, Zoom = zooming in/out.
Reset

Resets all parameters to their default values, in particular the y-axis scale factor to 25%, the shifting window size SW (if L>N: SW=2 *RoundDown[(L-1)/N] – 1 , otherwise SW=1 (N=# pixels of DiProGB window width; L=sequence length)), the start position to 1 and the end position to L.
List features

This button opens a window containing all annotated (and selected) features of the current mouse position.
To statistics

This button adds the average value of the displayed dinucleotide property (of the currently shown sequence part) to the statistics table (see 4.1).
Get sequence

This button changes the mouse cursor and, after selecting a certain sequence range, displays the corresponding sequence together with the sequence length and the A, T, G, C contents in a separate window (see 2.3 for more information).
Cancel

Closes the menu.

DiProGB provides various lists for searching, sorting and filtering the sequence information. The most important lists are explained in the following section.

2.2 Sequences, Dinucleotide properties

The list of preselected sequence files can be opened by clicking Sequence list in the right menu of the main window (7). The window is aligned to the left border of the main window and contains a list of path and file names of all currently selected sequences. Left-clicking on an entry in this list allows to change the actually uploaded sequence file and its features. The list is automatically filled with more than one entry when files containing more than one sequence are loaded, using the menu File->Open. Below the list of sequences are buttons for adding or removing sequences. It is also possible to open the currently selected sequence file with the standard editor (Edit) or to download additional sequence files from the NCBI homepage by clicking the download button.

Clicking on the DiPro list button opens a window aligned to the right border of the main menu which contains a number of preselected dinucleotide property sets. The dinucleotide property which is used for encoding the sequence can be selected by a left-click on the dinucleotide property name of the list (highlighted in blue). The selected dinucleotide property is then used for calculating the main sequence graph. 10 property sets are available in DiProGB by default. Further sets can be added by downloading them from the DiProDB database (clicking the Download button) or after creating own property sets with the editor (clicking on the Edit button). Additionally, the download page of DiProGB allows downloading of the 15 information carrying principal components representing the > 100 dinucleotide properties (cf. Friedel et al. Nucleic Acids Res. 37(2009) D37).
The first column of the dinucleotide property list allows to check all those properties that shall be displayed as additional sequence graphs above the main sequence graph (cf. 3.1 Sequence graph). After a property has been checked the color that is used for drawing the corresponding graph appears in the second column. This color can be changed by right-clicking onto the particular color. To check (or uncheck) all DiPros the user can click the ‘x’ in the header of the first column.

2.3 Feature list, selection

The Feature list contains all selected features and qualifiers available in either a Genbank file or feature file (.gff, .ptt,...). The first column of the table contains the names of the selected features. The second and third columns indicate the start and end positions. The fourth column indicates whether the feature is annotated for the + or - strand. The remaining columns contain other qualifiers (properties) for each of the features. The table entries can be listed in ascending or descending order by clicking on the column header. In the bottom part of the window a search option is available. By pressing the All button all hits for the search term are shown. In the list they are marked by a blue background and in the sequence graph start and end position of the hits are marked by red vertical lines. One can also ‘walk’ through the hit list step by step. This requires pressing the Next button.
All rows of the list can be selected by pressing the button Select all rows. To select one or several rows of the table the user can use the left mouse button. When pressing the Statistics button of the menu statistical information for either selected or for all rows is calculated and displayed in the Statistics table. The whole table or selected parts can be saved as a tab-separated text file by Save. Using Save one can also add the nucleotide sequence and/or the signal (calculated with the currently selected dinucleotide property) for each of the (selected) features as extra columns. Additional positions left and right of the feature sequence can also be taken into account.
The option Content->Add->Columns allows to add new features or qualifiers to the feature list (cf. 1.2 Feature files) and the option Content->Clear feature list deletes all loaded features and qualifiers. Cleaning the list has no effect on the uploaded feature or GenBank files.

The user can change the table content via the Content->Change selected Features and Qualifiers option. The corresponding interface shows all available features and the corresponding qualifiers. It allows the selection or deselection of specific features and qualifiers of interest which are then shown in the table and colored on the sequence graph. The interface contains 4 lists. In the first two lists on the right all different loaded feature names and the qualifiers of the currently selected feature are shown. The two lists on the left contain a subset of all feature and qualifier names. To select one feature and its qualifiers the user can double (left) click onto the desired feature name. After doing this the chosen feature and its qualifiers are automatically copied into the two left tables. Double (left) clicking onto an entry of the selected feature or qualifier list will remove this entry again. If the user wants to select all features + qualifiers he can also press the Choose all button. The Unselect all button will clean the lists of selected features + qualifiers.

2.4 Color list

The Color list displays all colors assigend to the annotated features or qualifiers of the displayed sequence. This list is automatically displayed when a new sequence is loaded into DiProGB. It can also be opened with Display->Colors. The color list also allows changing the colors or the Color scheme. The color scheme defines whether the colors are assigned to all the different features (this is default) or to specified qualifiers. The list of selected features and qualifiers colored on the sequence graph can be restricted using the button Restrict features/qualifiers.

2.5 Position information

This list displays all selected features and qualifiers annotated at the current cursor position. It can be opened by pressing the button Position info in the right side menu of the main window(8). The information is changing automatically when moving the mouse cursor over the signal. One can also open this list by pressing the button List features in the right mouse button menu. This opens the list in full screen showing all information available for the mouse cursor position. All features containing the position of interest are shown, ascendingly sorted according to their total length.

2.6 Marked regions

This table contains a list of all currently selected regions in the sequence graph. It can be opened by Display->marked regions and is updated automatically if a tool or the user changes the list of marked regions. The first column contains the name of the marked region, the second column indicates the strand where the marked region is located and the third and fourth columns contain the start and end positions of the marked regions, respectively. One can add new marked regions (Table->add->marked regions) or delete entries (Table->Delete). One can also mark all regions that were not marked before (Table->Invert marked regions). For all entries a mean value statistics (Statistics->Mean statistics) and a position-specific statistics (Statistics->Position-specific statistics) can be added. The menu entry Save->Table allows to save the table in a tab-separated file. For all entries a mean value statistics (Statistics->Mean statistics) and a position-specific statistics (Statistics->Position-specific statistics) can be added. It is also possible to calculate the percentage of the whole sequence or a selected feature that is covered by the marked regions with help of the region density statistics (Statistics->Region density statistics). The nucleotide sequence of one marked region can be obtained with help of the option Table->Get->Nucleotide Sequence for a selected region.