[Bioperl-l] frac_* methods

Jason Stajich jason at bioperl.org
Tue Oct 2 18:22:59 EDT 2007

I think my answer before was something to the tune of:

Use an alignment algorithm that finds a single best alignment like  
FASTA or Smith-Waterman (SW) if what you want is a single number that  
represents the alignment.  BLAST is great for fast searching but  
FASTA or SW/SSEARCH are going to be better at creating an alignment.   
Consider the -postsw option in WUBLAST as well as it will realign the  
HSPs with SW.

I personally never use the frac alignment summary stats for the Hit  
object for this reason unless I know I am going to have a single HSP.


On Oct 2, 2007, at 2:41 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
> -- 
> "Innovation distinguishes between a leader and a follower."
>     Steve Jobs
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
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Jason Stajich
jason at bioperl.org

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