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 > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
