ASP-N uses incorrect position in Cleave?

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?

Answer 1

[Luuk van Oosten]

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.

[Ryan Leib]

Hi Luuk,

Agreed, your proposed strategy works, and is what I've done to avoid the problem in my application.

My post was more error report than question, although its good that you've put in the strategy to avoid the problem. My concern was 1) that the error was general to other installs of matlab (I've checked 2 other installs at this point, all three have this error) and 2) that this be reported for a fix in a future update. Thanks again.

[Luuk van Oosten]

You are welcome. Have fun with your in silico protein digestion!