|New Mexico Supercomputing Challenge|
Challenge Team Interim Report
The problem we have selected deals with comparing sequences of amino acids for the protein actin in four different groups of animals. We will download and compare the amino acid sequences for one member of the class mammalia, one from aves, one from reptilia and one from amphibia. This information is already available. We will look at DNA sequences and try to determine where the exons and introns are and how the resulting amino acid chain is determined. We will compare the amino acid sequences and see how closely they resemble each other and how the differences increase as we move from one class to another.
After this part of the project is completed, we hope to download a section of DNA that has not had a sequence analysis done on it. This means that the locations of genes in the majority of the sequence have not been discovered. We hope to be able to study this information, label it and sumbit the sequence we discover.
Our progress up to this time is limited. We have found web sites that give us information for proteins and their sequence. These sites also lead us to protein sequences from other species. We still have not viewed or studied these sequences. We have not located or studied DNA sequences that have not been analyzed.
We are hopeful that we will be able to find and do a sequence analysis on a section of DNA that has not been completed. We hope that our study of the sequences of the classes of animals we select will enable us to do similar work on sequences that have not been analyzed. We hope to be able to identify the coding regions, the exons from the non-coding regions, the introns, and assign the amino acids to that sequence.
The main goal of the programmers is to use a network of computers to run the program. We wish to use MPI to run the program. We have located four computers to use and have installed Red Hat linux to be used for programming. Unfortunately, we have encountered several hardware problems that have limited our ability to proceed. A program has been written to analyze an artificial DNA data file, but this program does not use MPI. After we have the computers running again, we intend to modify the program so that it uses MPI.
For questions about the Supercomputing Challenge, a 501(c)3 organization, contact us at: consult1516 @ supercomputingchallenge.org
New Mexico Supercomputing Challenge, Inc.
80 Cascabel Street
Los Alamos, New Mexico 87544