Yes, if there are no decoys at all in the database and you don't want automatic decoys then the
empty string will disable it.
-Matt
On 3/11/2011 4:25 PM, David Shteynberg wrote:
Hi Matt,
Is it possible to turn off the decoy altogether in the search when
there are decoy in the database? I tried a search with DecoyPrefix =
"". Would that have the desired effect?
Thanks,
-David
On Fri, Mar 11, 2011 at 6:52 AM, Matthew Chambers
<[email protected]> wrote:
1. Yes. Set the DecoyPrefix parameter to whatever your existing decoys use.
2. Interesting question, since ProteinProspector's new pepXML export is not
really flexible about how the decoys are indicated (it's always with a short
'-' prefix and the decoy protein accessions are always trimmed so that
"sp|P00001|BLAHBLAH" becomes "P00001").
-Matt
On 3/11/2011 6:15 AM, Ben Collins wrote:
Hi,
I'm trying to use myrimatch as one of a number of search engines to
combine later with iprophet. It seems that later versions of myrimatch
are doing on the fly decoy database generation, because I tried to
search a database that already had decoys appended and ended up
doubling up on the decoys. So my questions are:
1. Is it possible to switch of the on-the-fly decoy database
generation in myrimatch so I can use a single database with decoys
already appended for all search engines?
2. If its not possible to change the myrimatch decoy behaviour, will
iprophet tolerate results from different search engines using non-
identical databases?
Many thanks for any advice,
Ben
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