My sequences are submitted; my options are set, how do I run a GEvo analysis?
Easy! Press the "Go" button at the top or the bottom of the web-page and you will see the phrase "Generating results. . ." in flashing red letters appear at the top of the web-page. Now, all you need to do is wait. Be patient as the results can sometimes take a while to generate depending on the length of the sequences compared, the size of the image you requested for your results, and the additional image options you selected. Please do not press the "Go" button repeatedly. This will send multiple requests for the same analysis and slow down the GEvo application server till all requests are processed.
One additional note: due to the nature of web 2.0 applications, all the parameter specifications you provided are still on the web-page. So after you get your results back and you would like to make a change (e.g. change the size of a submitted sequence), all you need to do is open the appropriate tab, make your change, then press "Go" again. Your old result is cleared from the screen and your new one will be there shortly.
Results of GEvo comparing a syntenic region of Arabidopsis from chromosomes 3 and 5 to a syntenic region of papaya. Gene models are the "arrows" nearest to the middle of a genomic region and are colored such that green or yellow is protein-coding regions (CDS exons), blue is mRNA (UTRs and untranslated exons), and red is the entire gene (exons and introns). Genes selected using the genomes database, CoGe, during sequence submission are colored yellow rather then green. Blast HSPs are numbered boxes and the number identifies the HSP in each genomic region. HSPs that appear above the gene models are in the (++) orientation and those that appear below the gene models are in the (+-) orientation. See "Understanding results" for more information.
Sometimes your results visualization can be improved if you "flip" your chromosomal regions left to right. In this way, genes from one genomic region can be ordered in the same direction as another genomic region. To do this, select the "yes" radio button next to "reverse complement" below the sequence submission menu and press the "Go" button again to re-run the analysis. In the example above, two regions were selected to be reverse complemented.
