[Bioperl-l] $hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Sendu Bala bix at sendu.me.uk
Thu Aug 3 14:34:01 EDT 2006

Andreo Beck wrote:
[re: frac_aligned_query, frac_aligned_hit]
> It still gives more than 1. Can you tell me how good approximation it 
> does? I mean if its 1.3 can I assume it 1 or something like that?

The only 'approximation' is to assume that none of the hsp alignments 
have gaps. It is still impossible for it to get more than 1. When you 
have gaps these methods are still useful because they give you a good 
idea of how much of the hit/query was involved in the alignment - not 
base for base but in terms of sequence coverage. So when they are 
working without any bug, the number returned is valid and correct from a 
certain viewpoint and shouldn't be 'fudged' like you suggest (treating 
one number as another (1.3 != 1)).

If it still does get more than 1 it is a bug that needs to be fixed. For 
the test data you sent me I get less than 1 now. Are you sure you 
managed to get and install v.1.16 or higher of 
Bio::Search::SearchUtils.pm ? Are you sure you are actually using the 
new module when you run your script?

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