Tip of the Week: GeVo and Genome Comparison

gevo_thumbToday’s tip of the week introduces a new (to us) tool for genomic comparisons. We came across this tool reading a blog post at James and the Giant Corn (great blog) about a figure from his research proposal. See, there are reasons to read blogs :D. The tool he uses to create this figure and analysis is GeVo at CoGe which has several useful tools in addition to GeVo. In today’s tip of the week, we’ll take a quick look at James’ figure at GeVo and introduce CoGe. Check them out, they look like quite useful tools. (and while you’re at it, check out  James’ blog. Tidbits like this and interesting discussions make it well worth it.)

3 thoughts on “Tip of the Week: GeVo and Genome Comparison

  1. James

    Thanks for the giving CoGe such a great plug Trey! (And it is great to hear you enjoy my site.) I was only introduced to it myself last spring, but it has completely won me over.

    One of the great things about CoGe is the interconnectedness of the tools. For example I could find a dna sequence using GenomeView or FeatView, click a button and send it to CoGeBlast, select which genomes to blast, select a couple of the most interesting hits from each of the genomes I’m interested in, click another button and send the locations of those hits to Gevo and get a visual appreciation of how the sequences compare with each other. From within Gevo, there are several ways to pick a part of the sequence (for example from within the full annotation link visible whenever clicking on a hit between two of the sequences) and send it back to CoGeBlast to search yet other genomes.

  2. Eric Lyons

    Hi. I’m CoGe’s lead developer and enjoyed this write-up on CoGe. Your GEvo tutorial is excellent, and thanks James for an excellent summary of how CoGe’s tools all are interconnected. This network of tools permits a variety of open-ended analyses without researchers having to work to get data from one tool to the next. Hopefully, this lets researchers rapidly explore genomic data in order to generate and test hypotheses. In any case, I wanted to add one tip to your GEvo tutorial which is that by holding the “shift” key when clicking on a blast hit, transparent wedges will be drawn between all the blast hits in that track. That way you don’t have to click on each one if you want to quickly see which parts of two sequences are similar.

  3. Pingback: Guest Post: CoGe, The Suite for Comparative Genomics – Eric Lyons | The OpenHelix Blog

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