I was wondering about software, which is able to say something about amino acids distribution of identified proteome and theoretical human proteome? I have gene name and uniprotkb accession number. I am looking for aa such as STY distribution etc.
Many thanks in advance,
Kambiz
If you want to study amino acid distribution in one or few proteins only, You can use protparam that'll tell you percentage of amino acids. But if you are looking amino acid distribution in whole proteome or a large data set, You need to download protein sequences and using an algorithm you can find the distribution of amino acids. On that basis, you can also assess which amino acids are preferred in the human proteome by comparing their observed frequency values with expected frequencies, taking into consideration codon bias also. There are also many articles published in this area to study amino acid distribution in certain specific organisms.
Dear freind what exactly u r looking whether the frequency of these stated amino acid or the patterns (strecth of amino acids that are having these amino acid residues).......
I am simply looking for frequency of AAs in proteome ... I have identified a proteome which has quit different pI compare to other human proteome ...
MEGA 5? I will look to it. However, Cytoscape is it not for protein-protein interaction map software?
Well, I have tried out the Protparam. This can not be used for proteome analysis. It is only for Single protein analysis. I do not know about MEGA yet. However, I will try it out. Thanks ... I am still interested in the software for whole proteome analysis ...
Kambiz,
I'm still not clear on what you want, or why you want it. Counting the amino acid symbols in a fasta file of protein sequences is easy. But what do expect to learn from the counts?
What I mean is, what is the frequency of distribution of different AAs in the proteome? For example, how often STY is expressed in the proteome? This will say something about ~P. I will than compare my identify proteome with background proteome.
A table of aa frequencies in whole human proteome is surprisingly hard to find!
There seem to be several resources on codon composition, combination of amino acids etc. which might be more suitable for you but if you want just amino acids try here http://www.pasteur.fr/~tekaia/aafreq.html
Well, it is not so difficult to get the AA distribution if you can a littel bit of computer programing. I can not. I got help for other nice pepole a cross the world they have done it. It can be seen on the following page: http://www.sharedproteomics.com/forum/showthread.php?473-Amino-acids-distribution-in-the-proteome&highlight=kambiz
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