AA Searches for homology between a protein query sequence and a protein sequence database. DNA Searches for homology between a nucleotide sequence query and a nucleotide sequence database. AA Searches for homology between the six possible translations of a nucleotide query sequence and a protein sequence database. Before you can run any of the programs, be sure to include the location of the programs in your PATH environmental variable. If you do not, you will have to specify the exact path to the programs.
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If the sequence contains multiple entries of the same name, you MUST use the -o F flags. The scores are explained in the release notes . Within those regions identified as homologous to previously determined coding regions, the relative rate of nonsense mutations is determined. If the nonsense rate in coding regions differs significantly from non-coding regions, then coding regions in the unknown are predicted by their codon preferences. Good scores are declared to be ORFs.