[Bioperl-l] frac_* methods

Chris Fields 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  
> list
> 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,  
> because
> 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 ?
> Best.
> Thiago

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