[Bioperl-l] SeqFeature::Generic 'frame' method

[Paul Gordon]

> Is it possible to get frame 0 in a TBLASTN match? I don't really know
> what this would mean. (for the risk of embarrassing myself, TBLASTN is
> DNA/DNA on the protein level, right? So you have a frame for both
> alignment partners, right?)
tblastx is dna/dna on protein level.  

<rant type="pedantic">
This has always irked me, since "t" indicates that the DB is being
translated, while in the blastp, blastn, and blastx the suffix letter
appears to indicate protein, nucleotide, and translated nucleotide query.
Implictily, n is nucleotide level comparison while p and x are protein
level, since no back translation is done in the program. 

By this reasoning tblastn, which does database translation against a
*protein* sequence should be called tblastp.  Though I suppose it's way
too late now for them to switch it...  anyone from the Blast team on
this list? :-)
</rant>

________________________________________________________________________
Paul Gordon                                     Paul.Gordon@nrc.ca
Genomic Technologies				http://maggie.cbr.nrc.ca
Institute for Marine Biosciences
National Research Council Canada