After a busy week and a weekend of violent sickness (food poisoning), you’d think I would take it easy for a while. Nope, you guessed wrong. I’m trying to learn BLAST.

Dramatic sigh goes here.

BLAST stands for Basic Local Alignment Search Tool. It is a set of programs that can either be downloaded or run through a web interface at NCBI. BLAST allows researchers to compare sequences of both nucleotides and amino acids. It can be used to deduce the function of novel proteins, determine what novel genes encode, find similar proteins, etc. Essentially, BLAST is an algorithm (actually, a set of algorithms) that can troll genome databases looking for similarities and return heaps of data.

Unfortunately, BLAST is by no means user friendly. Even after reading a few tutorials and playing around for a few hours I only have superficial knowledge of what I’m doing. I can run basic searches but any advanced queries (ie. the kinds I need right now) give me nonsense data or data I can’t understand.

I swore I would never get involved in Bioinformatics. It seems like a likely choice since I switched from Computer Science to Biology but I hate statistics, databases and everything Bioinformatics stands for. Unfortunately, it appears to be a powerful tool and it would be foolish to neglect it just because of personal opinion. And it might make me a more valuable asset in lab, which is good considering I am a lowly undergraduate trying to learn basic protocols.

My current plan is to purchase a copy of BLAST by Ian Korf and start pounding my head against the wall. I might get motivated and set up a dedicated Linux BLAST machine. My inner computer nerd is giggling with happiness.

Wish me luck. If you have any tips or are familiar with BLAST, please feel free to leave me comments. I’d love to hear from others!