Picture showing my foot very close to the edge of the Grand Canyon

Thrill of the edge: the North Rim of the Grand Canyon and me

In a post last January I shared how excited I was to become a participant in the Genome Education Partnership project. In less then 2 weeks I am bound to St. Louis, Missouri, to learn about bioinformatics (BI) as a project for crowdsourced research in education. I hope to document a bit my transition from a very superficial knowledge of BI to a deeper one, hopefully one adding a new dimension not only to my teaching, but also research.

My interest in BI came from my student’s interest in an obscure microbe and its even more obscure metabolic pathway. It has been a recurring pattern in my life that some of the most interesting things I learned (bringing me new avenues) came in a mysterious serendipitous way. So once he expressed his interest in having me as a thesis advisor (last Fall), I bought a basic BI book, started following people doing BI on Twitter, and filing articles away on Mendeley and Endnote. However, it was not until some days ago that I found enough space in my brain to actually start reading.

To clarify: if you know BI, you probably won’t find this interesting. On the other hand, I know that a lot of people do not learn certain things because they look intimidating, so they don’t even try. For years I avoided BI because I thought I could be a perfectly happy biologist without delving too deep into it…but the way things are shaping up, the next generation of biologist will need it. And as an educator of biologist, I should be teaching it then. Ergo, I need to learn more about it.

Back to the workshop materials: we were instructed to read the short article by Webber and Ponting for the definitions of the “-ogy” words, such as homology, analogy, orthology, paralogy, and xenology. While it is easy to say: orthologs arise from speciation, and paralogs from gene duplication; additional events such as deletion, duplications, conversions, and horizontal gene transfers (causing xenology) can make the picture quite complicated.  Sequence identity does not mean homology, although statistics (such as an E value lower than 103 ,provided by BLAST) and certain structural features strongly suggest homology.

Next, we were asked to work our way through some materials in the GEP website, such as BLAST tutorials, and introduction to Consed. I feel ok with Blast, although I will review the tutorials, but my next big leap will be to learn about finishing and sequence improvement.

Not today though.

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