Welcome to GEvo!

First, this help site is organized like a FAQ page, with each section (hopefully) answering a question on the functionality, under-workings, output and results interpretation of GEvo.

In a nutshell, GEvo is an application to facilitate the comparison of genomic regions using various alignment algorithms and display the results in a graphical output that is easy to interpret. The design principles are centered on making GEvo easy to use while providing the greatest flexibility to researchers and programmers alike. To accomplish this, GEvo coordinates the three aspects of comparative sequence analysis that are equally important to most researchers:

1: Sequence retrieval and sub-sequence specification

2: Alignment algorithm choice

3: Graphical visualization of results in context with sequence annotations

GEvo uses Web 2.0 design principles to create a more responsive, "desktop application" feel to the system. For those not familiar with these types of web-application, this means that areas of the web-page are dynamically updated as you interact with the system instead of the traditional approach where the entire web-page is reloaded between events (such as clicking on a "submit" button.)

Disclaimer: Please be aware that GEvo is currently beta software. This means that although it is still under development, it has reached a stage that we feel is useful for comparative genomics research. This also means that there may be bugs in the software that we are currently fixing as well as options and features that are still under development. Feel free to use our software and if you come across any problems or have any suggestions, we would would appreciate your feedback. Eric Lyons of the Freeling-Thomas collaboration is the primary contact for this project.

The image above is a screen shot of GEvo's interface showing the results of a three-way comparison using BLASTZ of a genomic region from rice with its two maize syntenic homeologs. The sequences were submitted using three different methods: retrieval from our in-house genomes database, retrieval from NCBI over the internet, and pasting in a sequence into a text box. Results are graphically shown on the top, with links to raw data files listed just below.