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.
