[Bioperl-l] SeqFeature::Generic 'frame' method
Tue, 27 Feb 2001 08:50:52 -0800 (PST)
On Tue, 27 Feb 2001, Paul Gordon wrote:
> 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? :-)
I'm not a BLAST developer. However, there's no where that says the suffix
refers to the type of comparison being done. Thus, the n in tblastn could
refer to the nucleotide database being translated. However, then tblastx,
which does protein level comparisons of translated nucleotide sequences
and databases doesn't fit.
So you're right. It's confusing.