genMod | R Documentation |
This function can be used to screen precursor masses for meaningful mass shifts which could correspond to post translational modifications. We suggest to only use a maxiumum of a handful of mass shifts.
genMod(sequences, modificationPattern, nModification=2)
sequences |
peptide sequences encoded as character sequence using the 20 amino acid letters. |
modificationPattern |
a rbind list structure containing the mono and avg mass as well as the description of a the modifications. |
nModification |
number of maximal modifications. |
t.b.d.
Hubert Rehrauer and Christian Panse 2012
ptm.0<-cbind(AA="-", mono=0.0, avg=0.0, desc="unmodified", unimodAccID=NA) ptm.616<-cbind(AA='S', mono=-27.010899, avg=NA, desc="Substituition", unimodAccID=616) ptm.651<-cbind(AA='N', mono=27.010899, avg=NA, desc="Substituition", unimodAccID=651) m<-as.data.frame(rbind(ptm.0, ptm.616, ptm.651)) genMod(c('TAFDEAIAELDTLNEESYK','TAFDEAIAELDTLSEESYK'), m$AA)
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