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

Jeffrey Chang jchang@SMI.Stanford.EDU
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.