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

[Téletchéa Stéphane]

Le 03/02/2014 22:39, Brian Osborne a écrit :
> Stephane,
>
> Do you see the same issue when "-displayname_flat => 1”?
>
> I’m talking about when you create $aln.
>
> Brian O.
Hum, sorry, forget about the duplicates names,
I should have done a proper verification, ...

There *are* duplicate names in my alignment, from the blast results
I transform all pass in fasta sequences for muscle, since there are
two pass -> two times the same sequence...

The other sequence stands true, though, I'm still getting
a 100% conservation for each position altough for
sure this is impossible to have such conservation amongst species
for a given protein ...

Any help on the "get id per position" code I'm using?

Thanks again,

Stéphane

-- 
Equipe DSIMB - Dynamique des Structures et
des Interactions des Macromolécules Biologiques
INTS, INSERM-Paris-Diderot UMR_S 1134
6 rue Alexandre Cabanel - 75739 Paris cedex 15 - France
Tél : +33 144 493 057
Fax : +33 147 347 431
http://www.dsimb.inserm.fr - http://www.steletch.org