Open-source software traces code of life Sept 4, 2008 8:59:21 GMT -5
Post by Bozur on Sept 4, 2008 8:59:21 GMT -5
Evolution of DNA: Open-source software traces code of lifedailygalaxy.com — There's a new computer program that knows all about your history - but don't worry, it's not going to report those parking violations. It cares about the evolution of your DNA. And it's open source. More… (General Sciences)
September 03, 2008
Evolution of Your DNA: New Software Traces the Very Code of Life
Human_genome There's a new computer program that knows all about your history - but don't worry, it's not going to report those parking violations or tell your friends what you do at night. It cares about your real history - the evolution of your DNA.
Researchers at Penn State have created the impressively named Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST to its friends - and yes, the team who are tracing the very code of life did just jam in an extra letter to make the name cooler). This software, when it's not hunting Doctor Who, can contrast and compare multiple protein sequences called 'retroelements'. These biological building blocks have existed for a long time, and since they make up half of YOU and many other things (genome-wise) they're pretty useful signposts.
The program can trace the relationships between organisms as varied as bacteria and HIV, producing an tree detailing the evolutionary "distances" between each. It compares every single pair of sequences, and without the subjectivity (not to mention boredom) of human experts performing the same task. Also, the program can operate in the less-than-25%-similar 'twilight zone' where other programs fear to tread.
Even better, these scientists are making the whole thing open-source - so that anyone who wants can trace phylogenetic pathways in their spare time (assuming they have access to a few million dollars of genetics laboratory). Okay, maybe it isn't the sort of thing you'll see people swiping into their iPhones (until society gets good and GATTACA'd up), but the concept of spending years on an amazing program, then just making it free because it's useful, is a great one.
The researchers also report that the program is learning rapidly as it acquires new data, and has already evolved considerably since they first activated it. But we're sure there's no danger in an evolutionary-minded, open-source and web-wide program that can do that.
Posted by Luke McKinney.
Evolutionary Distance Measurement
Official Paper (pdf)