The DECOY generator in the TPP is a fairly well tested tool and can be found under Decoy->Decoy Databases tab in Petunia. It expects that the input database contains only targets, and by default it retains the positions of all tryptic sites (thereby maintaining the target database peptide mass distribution) and shuffles tryptic peptides. There is alos an option to generate a reverse database.
-David On Wed, Jan 22, 2014 at 5:42 PM, srihari sharma <[email protected]>wrote: > 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]>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]. >>> 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]. > 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]. 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.
