4. GenomeComp tips and tricks

Chapter Contents
4.1 Customize the colors in the canvas
4.2 Zoom the display of comparison
4.3 Limit the length of matches
4.4 Skip the BLAST comparison process
4.5 Enlarge your eyeshot of the canvas
4.6 Remove items from the canvas

Customize the colors in the canvas

The default values of the color representation, island color and ORF color might not be the best you wish, but you can customize them before letting GenomeComp start the comparison. In some case you might wish GenomeComp to display all matches in the same color, there is a shortcut to realize it - just set the last value in the color representation list (the entry after "Below") to a very large number, so all the matches will be in this situation.

Besides the color setting for different length scales of matches, the values for distinguish every scales should also be customized for some different range of comparison.

New: In order to use your favorite color settings all the time directly, we highly recommend you to use the 'Save setting' function in the file menu.

Zoom the display of comparison

The graphical result of comparison is zoomable in the canvas by slide the slider in the figure scale bar to change the value. The default value is 10, which means that every 10 nucleic acid bases of the genome sequences are represented by one pixel in the canvas. Usually this value of setting can give you a very detailed information about the comparison. But it is necessary to increase this value for some large genome comparison to get a better globe view of the comparison result in the canvas. (The second example in the previous page is a good illustration.)

Note: Once the figure scale value is larger than 20, the text of ORF names in each genome will not be displayed in the canvas. Another default action is that, the ORF arrow will be replaced by a simply bar if the figure scale vaule is larger than 50.

Limit the length of matches

In genome-wide sequence comparison by BLAST there are usually tremendous "random matches" that are very short in length. So in GenomeComp we set a default lower limit of 100 bp to reject those short matches. For some case this setting can be increased or decreased for better result representation.

On the other hand the upper limit of the matches is not set, which means no limitation in default. But it might be useful for some special situations such as finding certain range of repeat sequences by self-comparison.

New: The matches length filter mechanism has been improved - users can just click the 'Apply' button in the main window to apply the new filter setting instead of redraw the figure. Hence, you can always use the default filter setting to draw the figure first.

Skip the BLAST comparison process

The most time consuming process for GenomeComp is the "BLAST comparison process" by calling the external programs from BLAST2 suite (especially for large genomes comparison). If you have to use GenomeComp to make the comparison between the same inputs once too often, this tips should be very helpful.

There is a mechanism in GenomeComp for skipping the BLAST if the program found the output file already exists in the working directory. Also for every comparison GenomeComp will save the BLAST output file in the working directory with file names look like XXX.out (for self- and paired comparison) or XXX.out.1 & XXX.out.2 (for three genomes comparison) by default (here XXX is the project name). Hence when redo a comparison if you set the working directory and project name in the configuration window just as same as the settings of the first time you did, you would be able to skip the BLAST comparison process for saving time. In other words, we recommend you choose a separate project name and working directory for each of the comparison project by GenomeComp. So you should can once for ado. (The first example in the previous page is a good illustration.)

On the other hand, you also can specify the output file name in the confirm window to make GenomeComp reading the comparison result from an existing file directly. But please make sure that the comparison result file is produced by BLASTN or MegaBlast and is in the correct format.

Enlarge your eyeshot of the canvas

The default GenomeComp window size is 800X600 pixel, so if possible try to set your minor resolution greater than this value to get a full view of the program window.

Even so sometimes you will still need to make the visible region of the canvas as large as possible, thus the hide menu should be useful. After GenomeComp finished the comparison process you can try to hide the control panel and then maximize the GenomeComp main window. Thus your canvas in the main window of GenomeComp will be as large as your screen.

Remove items from the canvas

New: Many accessorial items in the canvas (sequences title, ORFs, ruler, et. al.) are set optional from the view menu.

In some case, spurious matches that does not automatically filtered by GenomeComp or redundant matches caused by repeat regions et. al. might be very boring in the comparison canvas, especially when you want to output the figure. There is a special function in the program that can remove any items you dislike from the canvas.

Move your mouse to point and highlight the match in the canvas that you want to remove and just click the right button, so it will disappear! Pay attention that, this is an irreversible operation so you would have to restart the whole comparison process to retrieve the removed items.