[Biojava-l] Problem in Digestion with Symbol 'X'

[Andreas Prlic]

Hi Eman,

I think the error message tells you what is the problem.. what mass should
be assigned to X? You need to figure out what is the best way to handle
Xs...

Andreas




On Mon, Jun 17, 2013 at 11:24 AM, Eman Alhaweri <em.alhaweri at gmail.com>wrote:

> Hi
>
> I am working with Biojava in my Master project but I have problem and I
> hope if you can solve it for me. The protein database that I use in my
> project is contained Xs which is unknown symbol. When I tried to digest the
> protein sequences, Biojava gave an error that X is unknown symbol. Please
> tell how can the sequence pass the digestion without error.
>
> The error is: Exception in thread "main"
> org.biojava.bio.symbol.IllegalSymbolException: The mass of the symbol [VAL
> ILE GLY ALA CYS MET SEC GLU HIS THR PYL TYR SER TRP GLN PRO ASP LEU ARG LYS
> ASN PHE] is unknown
>
>
>  Thanks in advance.
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