You can find out if that is the case or not by running C:\Inetpub\cgi-bin\fastaidx.pl to create the .idx files if you have the web interface to sequest installed (or you can also generate the idx files from the web interface). That script calls some functions in C:\Inetpub\etc\fastaidx_lib.pl, which does the actual work. I'm running things through linux (and without petunia), so I can't easily do the testing myself, but I can lend a hand if needed.
Greg On Tue, Nov 11, 2008 at 6:49 PM, Olesya <[EMAIL PROTECTED]> wrote: > > Hi Luis, > I think it's a file format issue. Bioworks has 2 different fasta files > for each database - fasta and fasta.idx. I don't know what's the > difference between the two, but I figured out that they are both > required for Bioworks SEQUEST search. I took fasta ( the one w/o .idx > extension) file from Database Bioworks folder and generated decoy > database using TPP, but when I tried to do SEQUEST search Bioworks > didn't see my newly decoy generated file (I did transfer the decoy > dbase file from wwwroot folder into appropriate Bioworks Database > folder, so that wasn't the problem). > Thanks again for help. I am really excited I finally figured out how > to analyze data generated from Bioworks using TPP. It did take me a > day, but I can do it now. :) > > Olesya > > On Nov 11, 6:18 pm, "Luis Mendoza" <[EMAIL PROTECTED]> > wrote: > > Hello Olesya, > > Thanks for posting this. It would be nice if someone out there can > figure > > out why the TPP-generated reverse database does not work in Bioworks. > > Perhaps you have to register it first or a bad file format? > > > > Regarding your second point, the parameter is only optional if the > > "sequest.params" parameters file is already present *inside* the > > directory/folder that contains the .out files you are converting to > pepXML. > > This is not obvious from the interface; sorry about that. > > > > Cheers, > > --Luis > > > > On Tue, Nov 11, 2008 at 2:36 PM, Olesya <[EMAIL PROTECTED]> > wrote: > > > > > Hi all, > > > Just wanted to share a few tips with other Bioworks users: > > > 1) Thermo Bioworks can generate decoy (reverse databases) using > > > "Tools"->"FASTA database"->"Reverse". For some reason Bioworks' > > > SEQUEST does not recognize decoy databases generated by TPP. > > > 2) When importing SEQUEST .out files into pepXML one has to add a > > > Bioworks parameter file that was used for search. Currently this > > > option of adding parameter file has "optional" next to it in the > > > conversion window, but it doesn't work w/o the parameter file (at > > > least in my hands). > > > > > Olesya > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com 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 -~----------~----~----~----~------~----~------~--~---
