[bip] BLAST and FASTA performance

[A_user]

Everybody is speaking about algorithms. Not only the algorithms matters but also the speed of our programming language!

For example I have recently discovered a program called DNA Baser ( http://www.dnabaser.com/ ) which seems to be compiled, as it is only 1.5MB is size ( can be downloaded without registration ). 

They are using some very complex algorithm for sequence assembly and the accuracy of the results is amazing. This accuracy can’t be done using (fast) algorithms that are giving partial (poor) solutions. And still the program is incredible fast. 
So, if we don’t use a compiled language, at least we should spend some time to optimize our code for speed, not only to look for new algorithms because I have seen so many poor written Perl/Python programs….

Now, I decided to learn more about compilers. The dual code processor is already old on the market and the quadruple core will be here soon also. Compiled code can really take advantage of these new CPU features.