How can I customize the results image?


As the results image's goal is to help represent a complex set of information, GEvo does its best to provide an easy-to-read default view. However, depending on your comparison, you may want to adjust the image in order to better interpret your results. As such, we are constantly striving to provide more options that allow you to create a cleaner image of your results or add particular kinds of information so that you may be able to identify a new pattern in your data. Thus, you may have more options available than in the above example as this is an area of active development in GEvo.


To find the image options, click on the tab labeled "Image and Interface Parameters."


Here is a brief description of what each of these options do:


Image Width: Allows you to change the width of the resulting images. By default, this is set to 1000 pixels, but often you may want a larger image so that HSPs are not as crowded. Note, the larger the image you request, the longer it will take to generate.


Image Height: Allows you to adjust the height of the images.


Feature Height: Allows you to adjust the height of features (gene models, HSPs) within images.


Padding between tracks: The number of pixels used between each "track". A track is used to vertically place gene models and HSPs on the image. These images have the first track (that one which is closest to the dashed line in the middle of the image) used by gene models, and the second track for the first set of HSPs, the third track for the second set of HSPs, etc.


NOTE: The height of the image is dependent upon the height of the features, the size of the padding, and the number of tracks used to display the gene models and HSPs. For example, if there is only one pair-wise comparison, then two tracks are used, one of the gene models and one for the HSPs. If there are three pair-wise comparisons, each region is compared to two other regions and each image will have three tracks, one of the gene models, and two for each set of HSPs. Thus, if you change the feature height, the image height may be dynamically changed to accommodate the request.

What does the "color GC content" option do?


This options will color the background of the genomic regions according to the content of the underlying nucleotides. Specifically Gs and Cs are colored green, and Ns are colored orange. In the above example, you can see that coding regions tend to be more GC rich than non-coding regions (they are greener) and that there is an unsequenced region in the top genomic region (orange area). One thing to keep in mind is that generating images with GC content colored takes more time to render than images without such coloring. If you look closely at the image, you will also notice that the blast HSPs are no longer solid colors. Read the next question for an explanation. In addition, we are working on a motif-plotting algorithm that would mark and quantify genomic regions for a motif or sequence that you can specify dynamically.

What does the "color matches in HSPs" option do?


This options colors HSPs so that regions that match are colored and regions that don't aren't. This can be helpful for identifying which parts have high and low sequence identity, and can be informative when considering how three regions may diverge unequally.

What can I do to keep from being overwhelmed by the HSP numbers?


Sometimes you will do a genomic comparison where there are simply too many HSPs stacked on top of one another to get a clear idea of what is happening. In the above example, there is a duplication of a set of genes within an 80 kb region. However, in one region (the bottom genomic region) there was massive local duplication of some of the genes (highlighted by transparent orange boxes). As a result of this duplication, a given gene in one region matches many locations in the other resulting in too many HSPs being drawn on top of one another. To clean up the results page, we can use the "HSP Label options," "Limit HSP Labels," and "Auto adjust overlapping features."


HSP label options allows you to specify whether to draw the HSP numbers in the HSPs and, if so, whether to draw them all in the middle of the HSP or to stagger them so that they are draw in rotation at the top, middle, or bottom of the HSP.


Limit HSP Labels allows you limit the number of HSPs to get a label (e.g. the first 20).


Auto adjust overlapping features allows you to specify whether overlapping genomic features (such as HSPs) are drawn such that they take up a height inversely proportional to the number of overlapping features or whether to simply draw them all at the same height and to overwrite them when they overlap.

In the above example, the "auto adjust overlapping features" was turned off, and only the first 20 HSPs had their labels drawn in a staggered fashion. As you can imagine, it is easy to become overwhelmed by the amount of information that GEvo displays -- especially when comparing large genomic regions or regions with many local duplicated features. Addressing information overload is a priority for us in trying to improve GEvo.