MitoWheel 1.0: the human mitochondrial genome just got visual!
Posted by attilachordash on January 24, 2008
Your 16569 basepair long human mitochondrial genome does a lot for you and tells a lot about you. It encodes protein subunits playing crucial role in the production and conversion of ATP, the body’s main chemical energy currency. On the other hand the actual sequence of one’s mitochondrial DNA in a particular tissue or cell population gives a lot of health associated (mitochondrial diseases, aging) and ancestry information.
So far users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA. But now with MitoWheel version 1.0 (yes, it is beta) the situation is about to change. From now on you can spin MitoWheel and play MitoRoulette (details on the game later)! MitoWheel is a graphical representation of the circular human mitochondrial genome, hence the name. The sequence used is the standard Revised Cambridge Reference Sequence. The 3 main components of the app is: a search box, a sequence bar and the wheel.
MitoWheel is the brainchild of Gábor Zsurka, a human mitochondrial geneticist we’ve already met in the post on The power links of the mitochondriologist. Gábor has been doing 100% of the programming too. Disclaimer: With some suggestions and testing I qualified myself to become a member of the developer team! The wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript , a scripting language designed specially for Flash.
What are the basic things you can do with MitoWheel, if you are a scientist in the lab or a student in the seminar or just a tech geek eager to learn biology?
- spin the wheel: browse the genome by clicking the left and right arrows in the sequence bar
- search for a nucleotide position or sequence in the search box with numbers: input: 15450 output: T
the wheel and the sequence bar stops at the searched nucleotide position or sequence
and additional information (whether the nucleotide or the sequence is part of a gene or other specific region) can be seen on a pop-up window
- search for an encoded gene or specific region: for that you can use the abbrevations or shorthands of those regions, input: atp8 output in the search box and in the pop-up: 8366 A, 8366-8572 subunit of ATP synthase
- search for a nucleotide position or a sequence with nucleotides: input: ATGCTAAAA output:10760-10768
This is really just an elementary intro and I’ll uncover the plenty other features and tricks later. Hopefully a screencast will be added to.
All comments, suggestions, further ideas are mostly welcome, please email [mitowheel][at][gmail.com]
Jim H said
That is kewl. I am definitely not a mitochondrial geneticist, but had fun spinning the wheel all the same.
Elizabeth Dean said
Where can I find the geographical
distribution of mtdna haplogroup J*. All
I keep getting are hampsters and and snails! Especially interested in Irish population,human not rodents or mollusks.
Any suggestions?