FASTA on the Sun Grid

What is FASTA?

FASTA is a set of biological sequence comparison programs for searching protein and DNA sequence databases. More information on FASTA can be found here

FASTA on SUN Grid

Why?

Protein sequences and databases can be extremely huge. FASTA uses MPI to make the sequence search and comparison algorithms parallel in nature, meaning they can run simultaneously across multiple nodes. This makes FASTA an ideal candidate for the SUN Grid which is a network of high compute power nodes with MPI support.

How?

If you are expecting a FASTA download link and instructions to compile the source code, you have not realised the power of SUN Grid yet ;) FASTA binaries are already available in the SUN Grid's Application Catalog. All you need to do is check out FASTA from the catalog, prepare your set of inputs and feed it to the application! After checking out the job, see the details of the job for instructions on how to prepare the data and the corresponding fasta command with / without mpi support.

Sample Data

A sample data to test run the FASTA application can be found here.
This data resource contains many sequence / database files to test run both the MPI and non-MPI versions of FASTA.

Resources

FASTA HOME - http://fasta.bioch.virginia.edu
DEV.JAVA.NET - https://fasta.dev.java.net
SUN GRID USER GUIDE - http://www.sun.com/service/sungrid/SunGridUG.pdf


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