[Bioperl-l] trouble parsing swissprot annotations

Antonio Ramos Fernández tniram at hotmail.com
Fri May 21 03:05:40 EDT 2004

Hello, I have tried to parse annotations from a local copy of swissprot 
using Bio::SeqIO ($seq->get_SeqFeatures). I am interested in aminoacid 
prostranslational modifications, conflicts an variants.
I can extract primary tags (TRANSMEM, HELIX...) and locations ( start, end), 
but I cannot extract the string containing the name of the modification or 
the aminoacid substituted. This info is not contained neither in the tags 
nor as subfeatures. $feato_bj->display_name doesn't print anything (gives an 
error 'use of initialized value in print or ...').

How can I extract, for example 'MOD_RES 117 117 Phosphoserine' or 'CONFLICT  
232   232           G -> S ' withour having to build a new parser? (that is, 
I can't get the 'phosphoserine', which one is the right method?)

Dale rienda suelta a tu tiempo libre. Encuentra mil ideas para exprimir tu 
ocio con MSN Entretenimiento. http://entretenimiento.msn.es/

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