[Bioperl-l] frac_* methods
cjfields at uiuc.edu
Tue Oct 2 18:32:30 EDT 2007
I think their use is based on what you are trying to accomplish. For
instance I am currently running a lot of small BLASTN queries
(limiting by normalized bit score), so I tend to look at the HSP data
more. However, in other circumstances I might want the overall
frac_identical for all HSPs ($hit->frac_identical). YMMV.
On Oct 2, 2007, at 4:41 PM, Thiago Venancio wrote:
> Hi all,
> This topic was discussed before, but I would like to put it on the
> again, maybe someone has an update.
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP
> tilling. In
> my point of view, it is better to use it just in HSPs individually,
> there are some rare/strange kinds of alignments. However, we
> frequently need
> to get one measure of the whole alignment.
> Any of the BioPerl masters has an update on this topic ? What is
> the best
> current usage ?
More information about the Bioperl-l