newcompseq

There is more information in the Pipeline Readme but here is information specific to this program: 1) Blast all the individual 454 reads from the genome to the known drosophila genome assemblies available. In my case I BLASTed each of 4 different files filled with genomic DNA from 4 different Drosophila species to the genomes of Drosophila pseudoobscura pseudoobscura and drosophila persimilis.

The program I used to do this analysis is called newcompseq.plx. I wanted to run the program in parallel so I had to rename some of the temporary files that it opens. The 454 sequence reads that do not align to either one of the genomes are interesting. These interesting sequences are output to the designated file.