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SKILLS CLASS 2
DATE: FEB 10 - 2009
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Find all ORFs in human, chimp, and mouse mt-DNA
(GenBank accession numbers respectively NC_001807,
NC_001643, and NC_005089). Note that the genetic code
for mitochondria is slightly different from the standard one. In
particular the one for vertebrates has different start and stopcodons, resulting in different ORFs: the codon TGA meand
stop in the universal code, but codes for tryptophan in
mtDNA; AGA and AGG code for arginine in the universal
code, but for the stop-codon in mtDNA; and ATA represents
isoleucine in the universal code but for methionine in mtDNA.
What fraction of the sequence represents (candidate) protein
coding genes?
Repeat the ORF search on the randomized mtDNA
sequences. How long is the longest ORF that you find on
this randomized sequence?
Load the D. melanogaster gene eyeless from GenBank with
ref.nr: X79493, and H. sapiens gene aniridia at AY707088.
Study their global and local alignments and discuss their
statistical significance.
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