Hi jimmy, Thanks a lot for your reply. I got the decoy using the perl script.
The decoy from TPP petunia interface did not seem right. It was not reversing the sequence and also kept the REVERSED_ at the end of the sequence. Anyway the perl script has worked. Thanks a lot. Kind regards, Srihari Sharma On Wednesday, January 22, 2014 2:55:48 PM UTC+10, Jimmy Eng wrote: > > If you have the target/forward database, use the TPP's Pentunia interface > to generate the reverse decoy database. This will annotate the decoys > properly. > > Or if you have perl installed, you can issue a command like this on your > decoy database: > > perl -i -pe 's/^>/>REVERSED_/g;' decoy.fasta > > This is assuming you want "REVERSED_" as your decoy prefix. Using the > protein description in your original example, ">sw|P84710_REVERSED|", you > will end up with ">REVERSED_sw|P84710_REVERSED|" but this is fine. > > - Jimmy > > > On Tue, Jan 21, 2014 at 5:42 PM, srihari sharma > <[email protected]<javascript:> > > wrote: > >> Thanks a lot Jimmy. Is there a software tool or an online source that I >> can use to add a prefix? >> >> >> On Wednesday, January 22, 2014 1:20:39 AM UTC+10, Jimmy Eng wrote: >> >>> The decoy tag/names need to be the prefix i.e. >>> >>> >REVERSED_sw|P84710| >>> >>> In this example, enter "REVERSED_" in the input text box. There's no >>> way to do it with your existing decoy notation format so you are >>> unfortunately going to need to change your decoy entry names. >>> >>> >>> On Sun, Jan 19, 2014 at 5:27 PM, srihari sharma >>> <[email protected]>wrote: >>> >>>> Hello, >>>> >>>> I have a question with respect to decoy. >>>> >>>> The fasta files in my decoy files start as shown below, >>>> >>>> >sw|P84710_REVERSED| >>>> >>>> and my fasta files looks like as shown below >>>> >>>> >sw|P84710| >>>> >>>> Now the question is, while running the PeptideProphet step how do I tag >>>> the reversed fasta file as decoy. In simple terms what tag do I need to >>>> add >>>> in the below box for the reversed fasta file shown above? >>>> >>>> ->Use decoy hits to pin down the negative distribution. Decoy Protein >>>> names begin with: (whitespace not allowed) >>>> >>>> Thanks a lot, >>>> Srihari Sharma >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
