[Bioperl-l] Trying to get a conservation index out of a MSA

[Brian Osborne]

No problem, glad it works now.

On Feb 5, 2014, at 12:50 PM, Téletchéa Stéphane <stephane.teletchea at inserm.fr> wrote:

> Le 04/02/2014 20:48, Brian Osborne a écrit :
>> Stephane,
>> 
>> Can you send an example input file and complete script? You only showed a part of the script before, I think.
>> 
>> Brian O.
> 
> Dear Brian,
> 
> Thank you for your patience, it turns out the problem was with my blast parsing:
> 
> instead of using the $hsp->hit_string to get the protein sequence of my target,
> I created an alignment ($hsp->aln), and from this alignment, I took the sequence 1 using
> get_sequence_by_pos(1), which I assumed was the second sequence (the hit one).
> 
> After thinking two seconds, I remembered that bioperl is intellingent, and human aware,
> so it starts counting at one and not zero, so get_sequence_by_pos(1) is really the first sequence.
> 
> I have changed the parser to either use get_sequence_by_pos(2) or $hsp->hit_string and since
> both are equal, I'm now using the later :-)
> 
> Bad brain, sorry for the noise...
> 
> Stéphane
> 
> PS: if you take one template sequence + 500 identical "hit" sequences,
> this is then logical to get a 100% id for each position :-)
> 
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