*whoop* new project

gig'em crunchers

In conjunction with our 2 year anniversary..... already 2000 WU's done

nice! and very small requirements too....

(Added: The answer was posted in http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=10012#79080 )

Let me ask the same question in a more general setting.

Here is a brief article on BLAST which explains how it replaced the FASTA algorithm due to superior speed: http://www.the-scientist.com/article/display/15682/

Here is some information about PUMA2, a system for High-throughput analysis of (currently 1034) genomes which uses BLAST:
GADU – Puma2: http://compbio.mcs.anl.gov/
2005 TeraGrid News: http://www.teragrid.org/news/news05/gadu.html
2006 Nucleic Acid Research PUMA2: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D369

SIMAP ( http://boinc.bio.wzw.tum.de/boincsimap/ ) is described as follows:

The Fiocruz Genome Comparison Project will produce a database comparing the genes from many genomes with each other using SSEARCH ( http://helix.nih.gov/docs/gcg/ssearch.html ). Here is a brief description I found: SSEARCH - Performs a rigorous Smith-Waterman alignment between a protein sequence and another protein sequence or a protein database, or with DNA sequence to another DNA sequence or a DNA library (very slow).

I notice that each of these projects (Genome Comparison, PUMA2, SIMAP) uses a different algorithm (SSEARCH, BLAST, FASTA). What other similarities and differences do they have?

(Please note - I'm not complaining. I think that important scientific work ought to be done using many different methods to discover as much as possible and catch errors.)

Added: For the benefit of people reading this thread who are trying to learn more, I will post the URL for the Genome Comparison project description: http://www.dbbm.fiocruz.br/GenomeComparison

It begins:

Added even later: I have been thinking about Genome Comparison and SIMAP. Instead of just waiting for an answer, I'll throw out my most recent idea for public display.

( I must like to hear myself talk. I must have been insufferable back in the third grade. Come to think of it, I remember being surprised back in high school when I could not convince a schoolmate that there were no flying saucers and gave up the argument. One of the bystanders exclaimed that it was great to finally see me lose an argument. I had not thought of my arguing in that sort of way. After all - - I was always right! Just insufficiently persuasive some times. Ummm. . . . Perhaps I achieved my present state of perfection more slowly than I like to think. )

SIMAP compares proteins and Genome Comparison compares genes. Although there is a very close relationship between genes and the proteins that they code for, it is not a direct one-to-one relationship. The genetic code ( http://en.wikipedia.org/wiki/Genetic_code ) has several alternative ways to code for each amino acid in a protein. Even worse, there are some species that have modified the genetic code so that they produce non-standard amino acids in response to a genetic sequence. Just looking at the protein that is produced from a gene loses a lot of information that is present in the gene. So evolutionary relationships should be tracked using genes as the Fiocruz Genome Comparison project does rather than by using proteins from SIMAP. The functions performed by a protein are more likely to be the same in different organisms if they are closely related rather than distantly related.

This must seem obvious to anyone in the biological sciences. But I studied math and physics.

Added second thoughts: But according to the project description SSEARCH runs on the derived protein sequence, so it does not appear to use any genetic information directly. I guess I will have to wait for the explanation.