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FrFrequency of occurance of amino acids in natural proteins

Peter pxpst2+ at pitt.edu
Tue May 4 14:27:42 EST 1999

In article <19990423221603.93543.qmail at hotmail.com>, "Kaushik Raha"
<kaushik_raha at hotmail.com> wrote:

> Can anyone suggest me as to where can I find the frequency of
> occurance of amino acids in natural (wild type) protein structures. 

Blast can sort of do this.  If you look at the advanced blast you will see
an expectaion value, E.  This number relates a sequence you have versus
the probability of a random occurance of the sequence in nature.  This is
particular important when searching short peptides which will with all
likelyhood appear in many proteins and thus will be considered "not
significant" and thus not be reported. when dealing with polypeptides
longer than 20 amino acids, blast can do a far job identifing sequence
relatives.  Whether or not the sequence relatives are structurally
simmilar becomes a bit tricky.  NMR or crystalography is almost certainly
required for proof


" Don't you eat that yellow snow
     Watch out where the huskies go"

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