[lbo-talk] Kids! Compare Bio-sequence information with BLAST!

Dwayne Monroe idoru345 at yahoo.com
Mon Jun 11 12:58:40 PDT 2007


One of my operatives/friends happens to be a bioinformatic researcher working for a biotech startup.

An odd turn of the screw from my POV since I always imagined she'd wind up as a cruel yet lovely ruler of the Terran Galactic Empire we should have created by now (Lazy humans! Put aside your petty differences and get with the galactic conquest program already! Spectacular interstellar antimatter explosions await!).

A few days ago we chatted about my interest in (the still tentative and unproven) concepts of natural forms of computation which made her laugh because, as she put it, "sooner or later, serious gear heads like you always make their way back to the ancient machines" by which she meant everything from the wee beasties creeping along at the microscopic level to whales and every living thing in between.

"You really need to get into bioinformatics" she suggested "if you want to follow where the answers are likely to come from." Of course there's a Wiki article to get things started.

She introduced me to a software tool known as BLAST.

Wikipedia describes it:

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.

[...]

<http://en.wikipedia.org/wiki/BLAST>

Ah now that's just too beautiful - almost LCARS-esque in its cross referencing prettiness.

But wait, there's actually a free online interface provided by the National Center for Biotechnology Information:

<http://www.ncbi.nlm.nih.gov/BLAST/>

Oh brave new world that hath such algorithms in it!

.d.



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