I believe its only commandline enabled. This is something to ask the OMSSA developers.
-David On Tue, Nov 24, 2009 at 5:40 AM, Loïc JOFFRE <[email protected]> wrote: > 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. > 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. 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