Biology megablaster
Scientists love acronyms. Every project, every technique, every fancy new invention needs a good acronym. In fact, I once saw a presentation by a fellow researcher who openly admitted that she had named her project what she did just to have a cool acronym for it.
Today, I got to use a technique with one of the most powerful-sounding acronyms in all of science: BLAST. It stands for "Basic Local Alignment Search Tool," and it's used for matching DNA sequences. You enter your sequence into the website's search bar, select your parameters, and compare it to sequences in a database called GenBank. (I know, it's anti-climatic, but if it makes you feel any better, one of the parameter options is called "megablast.")
This story is going to sound a lot more exciting if I add "blast" sounds to each sentence. Here we go: I sat down at my laptop with the DNA sequences from coral larvae and spat I had collected with Hanny in Palau (blast!). I copied the first one into the search field on the website (copy-blast!). I pressed "search" and watched the page refresh every 5 seconds (waiting-blast!). The website returned a list of other sequences that matched mine, along with the percent match (results-blast!).
The top result was Montipora peltiformis, which is an Indo-Pacific coral (happy-blast!). The procedure worked, and I even got a reasonable result! The match wasn't perfect - only about 90% - so the coral larvae I had just BLAST-ed might not be exactly the same species but rather something related. I can conclude with a reasonable level of certainty that my larva is a plating coral in the genus Montipora.
Just to give you a reality check, I should mention that not every sequence I BLAST-ed had such a promising result. A number of them didn't match anything in the database, and for one of them, the closest match was a Canadian bighorn sheep (um, no). The usefulness of a database depends entirely on what's in it, so the most likely case is that no other researcher had sequenced the DNA of the species I was BLASTing. Coral larvae and spat are super small and difficult to identify by eye, so without a genetic reference, we may never know what species they are.
This story has four morals:
1) There is a lot of research left to be done, especially in remote parts of the world.
2) Acronyms rock.
3) Canadian bighorn sheep do not live on coral reefs in Palau.
4) Sometimes, hard work pays off in reasonable, exciting species identifications!
Today, I got to use a technique with one of the most powerful-sounding acronyms in all of science: BLAST. It stands for "Basic Local Alignment Search Tool," and it's used for matching DNA sequences. You enter your sequence into the website's search bar, select your parameters, and compare it to sequences in a database called GenBank. (I know, it's anti-climatic, but if it makes you feel any better, one of the parameter options is called "megablast.")
This story is going to sound a lot more exciting if I add "blast" sounds to each sentence. Here we go: I sat down at my laptop with the DNA sequences from coral larvae and spat I had collected with Hanny in Palau (blast!). I copied the first one into the search field on the website (copy-blast!). I pressed "search" and watched the page refresh every 5 seconds (waiting-blast!). The website returned a list of other sequences that matched mine, along with the percent match (results-blast!).
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| Hanny looking at some adult Montipora corals (white arrows) in German Channel, Palau |
Just to give you a reality check, I should mention that not every sequence I BLAST-ed had such a promising result. A number of them didn't match anything in the database, and for one of them, the closest match was a Canadian bighorn sheep (um, no). The usefulness of a database depends entirely on what's in it, so the most likely case is that no other researcher had sequenced the DNA of the species I was BLASTing. Coral larvae and spat are super small and difficult to identify by eye, so without a genetic reference, we may never know what species they are.
This story has four morals:
1) There is a lot of research left to be done, especially in remote parts of the world.
2) Acronyms rock.
3) Canadian bighorn sheep do not live on coral reefs in Palau.
4) Sometimes, hard work pays off in reasonable, exciting species identifications!
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