[Biojava-dev] Feature at position 0

[Tao Xu]

Hi there, 

I am trying to use SeqIOTools.readSwissport() to process a SwissProt flat file. An Exception is thrown whenever a feature at position 0 is encountered. The user manual from UniProt/SwissProt says that a feature at position 0 means the initiator methionine was cleaved off.
This happens quite often ( at least a few persent of the SwissProt records has this line "FT   INIT_MET      0      0". I googled and found your message. Is there a solution to this problem now? Thanks a lot for your help.

Regards,

Tao

On Wednesday 15 Oct 2003 2:11 pm, Mark Southern wrote:
> This is a real world example.
>
> Swissprot ID KAP3_RAT (AC P12369) is an example of a sequence with a
> feature entry at sequence location 0:
>
> FT   INIT_MET      0      0       BY SIMILARITY.
>
>
> This raises an IllegalArgumentException when the sequence is read in via
> SeqIOTools.fileToBiojava (see below).
>
> I don't know how oftem this would come up but its definitely a situation
> that isn't handled at the moment. Thoughts anyone?
>
Hmm, this one could be a problem - our coordinate system starts from one.  
What do they mean by position 0?  A cleaved methionine that's gone alreadY?

Maybe our code ought to have the option to skip these silently?

Regards,
David Huen