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

[Jeffrey Chang]

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.

Jeff