Hello David, I was looking everywhere on my OMSSA browser and in the OMSSA on line and I really do not see any option to output pepxml or any pepxml converter... Are you considering that .omx files are pepxml files? Because I could not use its on TPP... Could you give me the steps to output pepxml on OMSSA?
Thanks in advance, best regards, Loïc On Nov 23, 9:17 pm, "Vensel, William" <[email protected]> wrote: > David, > Thanks > Bill > > > > -----Original Message----- > From: David Shteynberg [mailto:[email protected]] > Sent: Monday, November 23, 2009 11:48 AM > To: [email protected] > Subject: Re: [spctools-discuss] Re: OMSSA files with PeptideProphet > > Hi Bill, > > Attached is a script and library dependency that will take two fasta > files and randomly interweave their entries. The idea is that one > file is your forward sequences the other is the reverse sequences, the > output goes directly to the console so you would have to redirect it > two a file. You have to use the commandline to use these tools. Copy > both files to one directory, and put your fasta files in the same > directory then open a commandline and switch to the this directory, > then you should be able to run this command: > > perl mergeFasta.pl forward_DB.fasta decoy_DB.fasta > merged_DB.fasta > > -David > > On Mon, Nov 23, 2009 at 11:36 AM, Vensel, William > <[email protected]> wrote: > > Hi David, > > > Could you please point to a tool that will allow randomization of the > > sequences in a fasta dayabase. > > > Thanks, > > > Bill > > > -----Original Message----- > > From: David Shteynberg [mailto:[email protected]] > > Sent: Monday, November 23, 2009 10:59 AM > > To: [email protected] > > Subject: Re: [spctools-discuss] Re: OMSSA files with PeptideProphet > > > Hello, > > > There is an option to output pepXML directly from OMSSA. Also OMSSA > > provides a pepXML converter. When you run the TPP on OMSSA results > > you have to specify the special option -P to InteractParser to fix the > > protein names in the OMSSA output, also the enzyme option should be > > given at the InteractParser step. To analyze OMSSA results with the > > TPP the current model requires the use of the non-parametric model, > > which requires Decoy in the database. Since OMSSA maybe biased in the > > order in which it reports equivalent hits, it is also recommended that > > you randomly order the sequences in your fasta database. > > > Hope this helps, > > -David > > > On Wed, Nov 18, 2009 at 12:41 AM, Loïc JOFFRE <[email protected]> wrote: > >> Thank you Brian, but I have already seen those post and they only > >> explain taht issues exist but no how to do. > >> If anyone knows? > > >> Thanks a lot, > >> Loïc > > >> On 17 nov, 17:04, Brian Pratt <[email protected]> wrote: > >>> I don't personally know anything about it, but a quick googling brings up > >>> this thread that may help you find someone who > >>> does:http://groups.google.com/group/spctools-discuss/tree/browse_frm/month... > > >>> - Brian Pratt > > >>> On Tue, Nov 17, 2009 at 6:08 AM, Loïc JOFFRE <[email protected]> > >>> wrote: > > >>> > Hello everyone, > > >>> > I have .omx result files (from OMSSA browser 2.1.1) and I would like > >>> > to use the PeptideProphet (TPP v4.3.1). > >>> > However, the PeptideProphet only accepts .pepxml files, how could I do > >>> > to run this process from my OMSSA result files? > > >>> > I have seen that a converter tool exist (omssa2pepxml) but I do not > >>> > understand how to use it, I have just found the source code of this > >>> > program on the web. > > >>> > I am working on Windows XP. > > >>> > Thanks a lot, > > >>> > Loïc Joffre > > >> -- > > >> 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 > >> athttp://groups.google.com/group/spctools-discuss?hl=. > > > -- > > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=. > > > -- > > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=. > > -- > > 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 > athttp://groups.google.com/group/spctools-discuss?hl=.- Hide quoted text - > > - Show quoted text - -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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