Report and Presentation

• project-final.pdf
• dmel-presentation.ppt

Scripts

• parse_intron.py - Split combined introns for each gene in the all-intron data files
• compareGenomes.py - Compare HMM ouput of a given motif for two species, printing an alignment of each gene ortholog, in descending order of summed HMM score.
• parse_orthologs.py - A naive approach to parsing the ortholog clusters from Inparanoid. Not robust.

Data Sources

• dmel-all-introns-4.2.1.fasta - All D. Melanogaster intron sequences, one entry per gene. (Directly from flybase.net)
• dpse-all-intron-r2.0.fasta - All D. Pseudoobscura intron sequences, one entry per gene. (Directly from flybase.net)
• ba.msa - B-A motif alignment used for HMM construction
• bb.msa - B-B motif alignment used for HMM construction

Program Output

• dmel-parsed-introns.fasta.gz - Output of parse_intron.py. Sequences of all D. Melanogaster intron sequences, individually named.
• dpse-parsed-introns.fasta.gz - Output of parse_intron.py. Sequences of all D. Pseudoobscura intron sequences, individually named.
• orthologs.txt.gz - Output of parse_orthologs.py. Pairs of D. Pse. gene names with corresponding D. Mel. gene names.
• dmel-ba-hmm.out.gz - HMMer raw output for motif B-A in D. Mel.
• dpse-ba-hmm.out.gz - HMMer raw output for motif B-A in D. Pse.
• dmel-bb-hmm.out.gz - HMMer raw output for motif B-B in D. Mel.
• dpse-bb-hmm.out.gz - HMMer raw output for motif B-B in D. Pse.
• compare-ba.out.gz - Output of compareGenomes.py for motif B-A.
• compare-bb.out.gz - Output of compareGenomes.py for motif B-B.