Question: Degenerate motif search - ScanProsite limitations
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gravatar for george.r.pope
4.6 years ago by
george.r.pope0 wrote:

Hi, I am very new to all this so please bear with me. 

The very basics of what I am trying to do is a peptide motif and find any occurrences of this in as near to the whole human proteome as possible.

So far I have been using ScanProsite and it has been fine. However, my most recent peptide motif is very degenerate, and when I search on ScanProsite it will not complete the search because of this. Personally however I would prefer not to alter my motif and get back thousands of possible proteins containing my motif and then do so extra sorting work upon those hits than start modifying my motif to begin with. I hope you all with me still.

I know you can download the ScanProsite database, but as I am new to this I am not sure what program I can run this through and whether it will help me out at all, regarding being able to complete a whole scan?

So I think the first things I would like help with if anyone can, are what program could I possibly use? Are there any other peptide motif sites that could help me? or (bit vague) are there any other solutions?

Thank you in advance for any help with this,

George

peptide motif alignment • 1.4k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by george.r.pope0
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