yes, those are the right steps On Thu, Jul 1, 2010 at 12:04 AM, Simon Michnowicz <simon.michnow...@gmail.com> wrote: > Jimmy, > thanks. So just to clarify, the process should be: > -take an existing sequence database > -create duplicate entries with reverse or randomized Amino Acid > sequences. Modify the Accession identifiers with <TAG>Identifier > -specify <TAG> when calling xinteract with the -d<tag> option > > With Mascot, we have to be format the reverse/random entries to have > the same FASTA header line format, so that Mascot Regex's can parse > them along with the original entries.. > > regards > Simon > > > On Jun 30, 12:37 pm, Jimmy Eng <jke...@gmail.com> wrote: >> You can use any prefix as long as it's consistent (and obviously >> unique and not present in the target database entries). In the tools, >> you will specify what prefix denotes the decoy entries. Like "REV" or >> "### "or "###REV###" ... >> >> On Tue, Jun 29, 2010 at 7:23 PM, Simon Michnowicz >> >> >> >> <simon.michnow...@gmail.com> wrote: >> > Dear Group, >> > I am trying to create a decoy database for use in the TPP pipeline. >> > I downloaded a Perl Script from Matrix Science, and noticed it put >> > entries like : >> > ###REV### >> > ###RND### >> > in Accession identifiers. However whilst looking at ISB slides noticed >> > that the Accession identifiers >> > are mentioned to be of the form “REV0” or “REV1”.‘REV’ >> >> > Is placing "REV' at the start of the protein name the standard way >> > of formatting Accession identifiers for use with the ISB tools (i.e. >> > protein prophet)? >> >> > thanks >> > Simon Michnowicz >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "spctools-discuss" group. >> > To post to this group, send email to spctools-disc...@googlegroups.com. >> > To unsubscribe from this group, send email to >> > spctools-discuss+unsubscr...@googlegroups.com. >> > For more options, visit this group >> > athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > >
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