yes, those are the right steps
On Thu, Jul 1, 2010 at 12:04 AM, Simon Michnowicz
wrote:
> Jimmy,
> thanks. So just to clarify, the process should be:
> -take an existing sequence database
> -create duplicate entries with reverse or randomized Amino Acid
> sequences. Modify the Accession identifie
Jimmy,
thanks. So just to clarify, the process should be:
-take an existing sequence database
-create duplicate entries with reverse or randomized Amino Acid
sequences. Modify the Accession identifiers with Identifier
-specify when calling xinteract with the -d option
With Mascot, we have to be f
> The entire database is reversed. They're all decoys. A search engine
> is run on the original database and then run again on the reversed
> database.
My two cents: In the TPP world, we generally use databases with
reversed or othewise decoy entries appended to the primary entries.
I'm not certa
> So how do you know if the protein is a decoy or not?
The entire database is reversed. They're all decoys. A search engine
is run on the original database and then run again on the reversed
database.
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Hi Jesse,
So how do you know if the protein is a decoy or not? The decoy prefix is a
widely used convention because it keeps the accession unique and is very
unlikely to get cut off from the accession in a token split between the
accession and the description.
-Matt
On 6/30/2010 11:23 AM
The decoy databases we use have no additional tags. It simply reverses
the sequences.
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