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 at >> http://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 at > http://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 at > http://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 at http://groups.google.com/group/spctools-discuss?hl=.
FAlite.pm
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mergeFasta.pl
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