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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