[EMBOSS] Emboss-Digest

[ajb at ebi.ac.uk]

Dear Sudeep,

Trypsin doesn't cut as well if (e.g.) the K is followed by any of
"KRIFLP" (Prof. D. Pappin, personal comm). Your sequence contains
"...KL..." so there is no cut. If you want unfavoured cuts to be
shown (e.g. a cut after every K for trypsin) then add the flag
"-unfavoured" to the command line.

HTH

Alan


> Hello,
> I used "digest" from EMBOSS to digest protein database obtained from
> NCBI REFSEQ.
> Here is how I executed digest:
> digest -seqall "DB_NAME" -aadata "File_name"- outfile "File_Name"
>  From the list I selected trypsin
> For some reason, digest skipped (no fragments were generated) for this
> particular protein
>  >gi|118430285|ref|YP_874719.1| photosystem II protein K [Agrostis
> stolonifera]
> MPNILSLTCICFNSVLYPTTSFFFAKLPEAYAIFNPIVDVMPVIPLFFFLLAFVWQAAVSFR
>
> any ideas?
>
> I should get two fragments. I don't want to see the partial digests so
> that is why I never selected the option.
>
> Thanks
> Sudeep
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