The yellow bar next to the locator is called the summary bar: it represents the DNA sequence and, and with the appropriate window settings, can be used to display various features such as restriction sites. Its scale (in base pairs) is given by the bar on its right.
Some information is given on the right side of the window, including the name of the gene and its literature reference and labels indicating various sequence features (TATA box, poly-A signal). Additional information can be obtained by double-clicking on these data items to bring up relevant text windows.
One line of information about the currently selected item is given at the top of the window (highlighted in blue on colour screens).
The type of information displayed in the window depends on the data available for the sequence and the settings of the sequence window. In this case, the program displays graphical representations of the features listed in the GenBank database entry for this sequence. These include the intron-exon arrangement of the gene, and various DNA signals (e.g., TATA box, polyA signal) indicated by small violet boxes (these may not be visible on a monochrome screen)
These features are labelled on the right side of the window. The labels and the graphical representations are linked: clicking once either on the graphical representation or on the label highlights both, and displays some additional information at the top left of the window (under `Selected DNA').
A lot more information can be displayed in this window by changing its settings using the Columns button.
* Click on the Columns button.
The various types of information which can be displayed (when available for this particular sequence) are listed here. The currently selected data types are highlighted in blue. These include the locator, the scale bar, the summary bar and the text features (the features listed in the feature table of the sequence record). Some data types are highlighted but do not appear in the sequence window because no such data is available for this particular sequence (for example, inverted and tandem repeats).
* Click on Text Features and on Scale.
These items are no longer highlighted and will not be displayed when the Return to display button is clicked.
* Click on DNA Sequence.
This item is now highlighted.
* Click on the Return to display button.
The scale bar and the various features are no longer displayed. They are replaced by a DNA sequence and a new button enabling the user to set the number of sequence characters to display per line. Because the current window magnification is too low, the whole sequence cannot be displayed. The ellipses (...) at the end of each line indicate that additional sequence exists but is not shown.
* Click once on one of the exons in the exon-intron graph.
The corresponding sequence is highlighted in the sequence listing.
* Experiment with the Columns button to see the data types that can be displayed in the sequence window.
The program can display many features and views of the gene, including start and stop codons, open reading frames, protein translation etc.
* When finished, select the following data types to be displayed: Locator, Restriction Map, Summary Bar, Coords and DNA sequence.
* Click twice on the Zoom In button.
This magnifies the screen to a level where the whole sequence can be displayed and the ellipses disappear.
* Click on the Clear button to remove any highlighting.
* Click on the Zoom Out button twice to return to the original magnification.
* Click on the Set DNA Width button and change the displayed width to 50.
* Open the pop-up menu and select the option Analysis window.
This brings up a new window offering a number of options for sequence analysis. The following example demonstrates how to simulate a restriction digest of the selected gene with HindIII and EcoRI.
* Click on the yellow box and type in the enzyme names separated by a semicolon: hindiii ; ecori.
* Press <return>.
The sequence window is brought back to the foreground. The specified restriction sites are highlighted in the sequence (when they are in a currently displayed part of the sequence) and are indicated by slashes on the summary bar.
* Click on the Clear button to erase the restriction digest results from the sequence window.
* Bring the DNA Analysis window back to the foreground.
The results of the restriction digest (cutting sites and fragment sizes) are shown in the lower part of this window (you may have to change the size of the window to see it all).
* Click on the Show gels button.
A new window titled Agarose Gel appears.
The controls in this window are similar to those of the genetic map window (coarse and fine control sliders, Zoom In, Zoom Out and Whole buttons). For the time being, no data are displayed in the window. Restriction enzyme names can be typed in the yellow text entry box near the top right corner of the window.
* Click on the text entry box and type in hindiii; ecori then press <return>.
A series of bands appear in the window. They simulate an agarose gel on which the specified digest has been electrophoresed. A second restriction enzyme entry box appears underneath the first one to allow the specification of a second digest to be displayed in another lane of the gel.
Note: the specified restriction sites are also shown in the sequence window.
* Click on the Coordinates button.
Each band is now labelled with the length of the corresponding restriction fragment in base-pairs.
* Double-click with the leftmost mouse button on the band corresponding to the largest fragment (1541 bases-long).
* Bring to the sequence window to the foreground.
The part of the sequence corresponding to the selected band is now highlighted in dark blue, both in the summary bar and in the sequence listing.
* Click on the Clear button.
The remaining buttons of the sequence window are the Reverse Complement button, which changes the sequence to its reverse complement, and the Genefinder button. This button is in fact a pop-up menu and must be opened using the rightmost mouse button. It allows access to an automatic gene finder utility to detect coding sequences by codon usage, splice site and open reading frame analysis. However the functionality of Genefinder is limited when `browsing' through ACeDB because some of its commands modify the database and are restricted to the database editors.
* Use the Quit option in the pop-up menu to close the sequence window.
* Click in the main ACeDB window with the rightmost mouse button and select Clean up in the pop-up menu.
This closes all ACeDB windows except the main window.
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