David, Do you know a version of Myrimatch that runs smoothly with the current release of TPP? I have definitely gotten this to work with much older version of Myrimatch in the past but it seems like the Myrimatch pepXML has been evolving and the current version of Myrimatch causes problems for xinteract (at least in my hands). If you're interested in more details on the error I can provide them, but I would also be very happy to run with a little older version of Myrimatch if you have one running with TPP 4.4.1 at ISB.
Many thank, Ben On Mon, Mar 14, 2011 at 3:41 PM, Matthew Chambers <[email protected] > wrote: > 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 >>>> >>>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "spctools-discuss" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]. >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >>> >>> >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
