The purpose of GEvo is to compare multiple genomic regions from any number of organisms using a variety of different sequence comparison algorithms in order to quickly identify patterns of genome evolution
To alternate between areas to configure an analysis, select the appropriate tab.
Select the "Sequence Submission" tab to open these options. Here, you can specify sequence submission boxes for each sequence that will be submitted for a GEvo anlaysis. This is also were you can adjust the amount of sequence analyzed, select which sequences are analyzed, reverse complement a sequence, mask a sequence according the the genomic features it contains, and change the display order of sequences.
To add another sequence submission box, press the "Add sequence" button. After pressing, a new sequence submission box will appear
There are three types of ways that you can submit a sequence to GEvo:
You can select the sequence submission type from a drop-down menu located next to the name header in a sequence submission box. E.g.: Sequence 1.
Each sequence allows you to specify the amount of sequence to be analyzed.
If you want to change all the positions of CoGe submissions at once (e.g. add 1000000 nt left and right of all sequences), just type in the amount of sequence into the box next to "Apply distance to all CoGe submissions".
Likewise, you can do something similar with the box next to "Pad CoGe Sequences with additional sequence". However, when the results are returned, the position slider bars are positioned based on the amount specified, not taking into account the amount added through padding.
After a preliminary GEvo anlaysis, you may want to drop a sequence from the analysis. For example, if the region is repeated in another submission or if there the pattern you were seeking is not present (e.g. synteny). To skip a sequence, just select "yes" from the row "Skip Sequence" in the options shown at the bottom of each sequence submission box.
A reference sequence is one to which all other sequences are compared. By default, all sequences are selected as reference sequences. However, you may wish to only specify a couple of reference sequences. For example, you are searching for syntenic regions from genome B to genomic region A. By turning off sequences as reference sequences, the number of pair-wise comparisons is minimized so the analysis is processed more quickly. Also, this can help simplify visualizing and interacting with the results. Especially if one genome has lots of repetitive sequences.
After a preliminary GEvo analysis, you may want to "flip" a sequence. To do this, select "yes" for the row "Reverse complement" located at the bottom of the sequence submission boxes.
This option allows you to mask a sequence based on its annotated genomic features:
Sequences are displayed according to the order of the sequence submission boxes. To change this order, just click and drag the title of a sequence submission box into a new position.
Current GEvo can use:
GEvo supports using Chaos, BlastN, and BlastZ for seeding DiAlign.
Of these algorithms, blastn and blastz are the two that are most useful for most people. These two algorithms are local alignment algorithms and will find regions of sequence similarity located anywhere between two sequences. The primary difference of these algorithms in terms of their utility are:
Use blastz if you are comparing large genomic regions and/or looking for synteny by identifying collinear series of genes Use blastn if you are comparing gene models, analyzing exons, searching for CNSs], or looking for conserved motifs
GEvo's results are displayed in an interactive system called gobe that lets you connect regions of similar sequence, and get additional information about genomic features. Please follow this link for more information about gobe.
Each panel represents a genomic region, with the dashed line in the middle separating the top and bottom strands of the chromosome. If gene models are present, they are drawn as composite colored arrows above and below this line if they are read from the top and bottom strand respectively. Usually, the full gene is the gray arrow, on top of which is the mRNA (blue), on top of which is protein coding sequence (CDS). There are other colors and icons that represent other types of genomic features that are described [[GenomeView_examples | here]. Above and below the gene models will be the identified regions of sequence similarity. These are represented by colored boxes. The location of the colored box above or below the dashed line signifies of whether the match is in the (++) or (+-) orientation respectively. Each pairwise comparison will have its regions of sequence similarity drawn in a separate track (both above and below the dashed line) and are usually different colors from one another (though that is configurable). To see which region matches which other region, just click on a colored box, and a transparent wedge will be drawn connecting it to its partner region. For more information about GEvo's interface, see the documentation on gobe.
After results are generated by GEvo, a URL will be created that will be a hyperlink to GEvo with your analysis pre-configured. To regenerated the results, all you need to do is press the "Run GEvo Analysis!" button and wait for the analysis to run. This link is stored in two places:
GEvo Direct is a tool for quickly viewing the results of a previously run analysis without having to re-run the analysis. Please Note: CoGe saves all the files from a GEvo analysis for ~24 hours. After that time, the data-files are deleted and the GEvo Direct link will no longer work.
Registered CoGe users can save a link to a GEvo analysis for later retrieval from their work history. This permits a GEvo analysis to also be names and annotated for future reference.
Some genomes have contig assembly information. To view this in GEvo's results:
If you want to have the HSP number drawn on the HSP:
If you want to have the feature names drawn on the feature:
By default GEvo will drawn overlapping genomic features and regions of sequence similarity on top of one another. However, this sometimes hides some of the interesting complexities in a genomic region such as local duplications or regions containing repeated sequences. To view these, select the "Results Parameters" tab and select "Yes" for "Auto adjust overlapping features" and/or "Auto adjust overlapping HSPs". These options are set to "No" by default because finding and drawing overlapping features can take a long time to process, and are not always useful.
Often, there are times when you will want to merge together two or more separate GEvo anlayses. To do this, copy a GEvo link into the text-box next the text: "Merge Previous GEvo Analysis (paste in URL)" located at the top of the sequence submission tab. Then press the "Merge" button". The sequences as specified in the pasted URL will appear as new sequence submission boxes configured as specified in the link (extra up/downstream sequence, reverse complement, masked, etc.)
Once a GEvo analysis has run, you can change any of the analysis parameters and re-run the analysis by pressing the "Run GEvo analysis" button again. The common parameters changed are:
Comparing sequences with lots of common sub-sequences usually causes GEvo to take a very long time processing the analysis (both in terms of identifying the common sequences and generating the final results). Also, if many regions are identified, it is often difficult to make sense of the results. This kind of problem will surface in many large genomes, such as mammal and plant genomes. For example human and maize are both riddled with large amounts of repetitive sequences derived from retroviruses and transposons. This makes the comparison of large genome regions in these genomes difficult, if not impossible. To circumvent this problem, mask all sequence that does not code for protein. You can select this option under the "Sequence options" menu and selecting "non-CDS" for the row "Mask Sequence".
Linking to GEvo is easy! Please see this page for how to do this.
Please see exporting GEvo results for publication for how to do this.