Basic operations with DNA molecules.

The interface of Gene Studio consists from menu bar, which allows to make all operations, toolbar, graphics panel and text area. Menu contains all the functionality of Gene Studio. Toolbar has several buttons for the most frequently used features and a text field, which shows the selection range or cursor position in the text area. The content of this text field can be copied by context menu "Copy" or by selecting needed symbols and pressing Ctrl+C. Graphics panel shows graphical representation of DNA molecule and text panel shows the DNA sequence from 5' to 3'.

Editing sequence. To Open File go to menu File>Open... or press Ctrl+O. Select file in the dialog window and press "Open". To save file use menu File>Save or menu File>Save as if you want to save file under another name. To close currently opened file use menu File>Close.

Gene Studio allow to edit gene sequence in the text area, copy and paste sequences. To copy sequence press Ctrl+C or use Edit>Copy. The same can be made from the context menu. The sequence will be copied to the clipboard without white spaces that present in the text area. To cut the sequence can be used menu Edit>Cut, Cut menu item from context menu or Ctrl+X key combination. The paste of a sequence from the clipboard can be done by pressing Ctrl+V, by activation of menu Edit>Paste or "Paste" in the context menu. If the text in the clipboard does not contain symbols which can be used in the DNA sequence, such symbols will be omitted in pasted text. Symbols valid for DNA bases designation are shown in the table 3. Symbols other then A, T, G, or C are wildcard characters.

Table 3. Nucleotide designations.

SymbolNucleotide(s)
ADeoxyadenosine
TDeoxythymidine
GDeoxyguanosine
CDeoxycytidine
RA or G
YC or T
MA or C
KG or T
SC or G
WA or T
HA, C or T
BC, G or T
VA, C or G
DA, G or T
NA, T, G or C

It is possible to invert the DNA sequence which should be pasted. For this purpose menu Edit>Paste inverted can be used or the same named menu item from the context menu can be used.

To rename opened molecule use Edit>Rename. In the appeared dialog box enter new name for the molecule and press "OK".

Gene Studio stores five changes made in the DNA molecule and these changes can be reverted by Pressing Ctrl+Z or by using menu Edit>Undo. If changes were reverted as a mistake, it can be returned by pressing Ctrl+Y or menu Edit>Redo. Replacing DNA sequence by selecting it and pasting another one in this case considered as two events: cut and paste.

Making picture. To make a picture of a graphical view of DNA molecule use "Take picture" toolbar item or menu Edit>Make Picture. Gene Studio supports PNG, JPEG, GIF and BMP picture formats.

Work with Features. To mark a feature on DNA molecule select the region, which is intended to be marked, and press Make Feature item in the context menu or Edit>Make feature in main menu. In the appeared dialog window enter the name of a Feature, check if begin and end of feature are marked correctly. Note that begin may be more then end on the circular molecules. The type of feature can be changed in the "Type" drop down box. Uncheck the check box "Direct strand" if feature is located on the reverse one. To make feature to have color other then default, select color from the standards in the "Color" drop down box, or select the color from the palette. To select the color from palette press "Change". After all changes was made press OK button. After feature has been created, it can be changed by selecting it and using Edit>Edit feature or "Edit Feature" context menu item. Feature can be selected by clicking itself, by clicking it's name on the graphics panel or by selecting the region feature locate in the text area. To delete feature, select it and activate menu item "Delete Feature" from the context menu or from menu Edit.

Search. To search sequence on the DNA use Ctrl+F or Find menu items in menu Edit or on context menu of graphics panel. In the appeared dialog window enter the sequence to be found and press Find button. The program will highlight the first matched sequence from the beginning of molecule. If the sequence to search will not be changed, consequent searches will find next matches if any. After all matches finished the first match will be shown. Case of letters is not necessary.

If the molecule contains a lot of features, it may be useful to search through feature names. It can be done from "Find feature" item in the context menu of graphics panel and from menu Edit. In the dialog window enter the feature of interest name and press Find button. Program will show the first feature which contains the entered string in the name. Case of letters is not necessary. As in previous case if string to search for was not changed, the next match will be shown. If the end of molecule was reached search will resume from the molecule begin.

Making DNA circular/linear. To make DNA circular press button "Make circular" on the toolbar or in Properties menu put mark next to "Circular". The begin of circular molecule located at the top of circle (90°), sequence has clockwise direction. To make DNA linear the same operations should be made with "Make linear" toolbar button or "Linear" menu item in Properties menu.

Setting up view properties. The view properties of the molecule define how it will be presented in graphics panel. It can be changed from menu Properties or partially from graphics panel context menu. To hide features select menu item "Show features" on context menu or in menu Properties. To hide only ORF (available only if features are allowed to be shown by previous item) select menu item "Show ORF" on context menu or in menu Properties. The same way "Show restriction sites" menu item is responsible for showing of restriction sites. To show features again put a mark next to "Show features", "Show ORF" and "Show restriction sites" in case if restriction sites should be shown.

Another view parameter which can be seen in text area is grouping. By default each string in the text area presented by 60 nucleotides grouped by 10. Alternatively nucleotides can be grouped by three nucleotides. To change this - put mark against intended grouping order in menu Properties "Group by 10" or "Group by 3".

Finding ORFs (Open Reading Frames). Finding of open reading frames can be done from menu Analysis>Find ORFs or from the same menu item of graphics panel context menu. After activation of these menu item the dialog window will show up. In this window user can change minimal and maximal length of ORF and also triplets which can be used as start. The button "Reset" resets these search parameters to their default values. To begin search "Search" button should be pressed. If ORFs were found it will be shown on the map. To see them "Show ORF" and "Show features" should be checked in the graphics panel context menu and in menu Properties.



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