ASP-N uses incorrect position in Cleave?
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Hi,
Using the cleave() function, ASP-N is stated to cleave at position 2 by cleavelookup(). However, this should be clipping at position 0 (n-terminal of D residues). Can someone else verify this is functioning incorrectly?
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Luuk van Oosten
2014년 11월 24일
Dear Ryan,
I am no expert, but I've used the cleave function before to make an in silico tryptic digest and also had some troubles using the MATLAB build-in codes for cleavage; confused me as well.
What I eventually did was use the following (and this is clearly explained in the help docs as well):
you want to use cleave and produce fragments (I presume.... your question lacks a lot of info...)
Fragments = cleave(SeqAA, PeptidePattern, Position)
so, for 'SeqAA' you put in the sequences you want to cleave. For 'PeptidePattern' you would want to use 'D' (cleave at an aspartic acid), and if you specify 'Position' as '0', it would cleave your sequences exactly as you described in your questions;
so:
SeqAA = yoursequences;
PeptidePattern = D;
Position = 0;
yourfragments = cleave(SeqAA, PeptidePattern, Position)
I guess that would do the job, but you should try it out for yourself; I have no idea what you want to do.
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