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 <[email protected]> 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 > > > > <[email protected]> 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > 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 [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=en.
