If there's some set of unique identifier in the original database that denotes all the proteins you want in the subset database, you can use the subsetdb program. It's distributed as part of the TPP (typically binary exists at c:\inetpub\tpp-bin\subsetdb.exe) but there's no web interface to it that I'm aware of.
As an example, to create a drosophila subset of the uniprot database, you do something like: subsetdb.exe -MOS=Drosophila^melanogaster -ofly.fasta uniprot_sprot.fasta This creates an output file "fly.fasta" that contains all entries with the text "OS=Drosophila melanogaster" in the protein description line. The carat (^) character replaces a space. You can have multiple -M match text string options, no match -N strings, etc. Typing the executable w/o input arguments will show the usage statement. On Thu, Oct 21, 2010 at 4:41 PM, Kristian <[email protected]> wrote: > Okay. To do that, all you can really do is make a smaller data base. > There's no function in the TPP that will allow you do select a subset > of your database. However, it's really easy to edit your database. > Open your database in a text editor (i.e. wordpad) and you'll see the > format the entries have. Use this format to create a new database > that only contains the entries you are interested in. Note that > searching against a small database will compromise your statistics > (partly because if you're only only searching against a small number > of possible matches, X!Tandem will probably find something that > matches it, even if poortly; and partly because Peptide Prophet's > error model works best if there is a large number of incorrect hits as > well as correct hits. ). For the best results, add decoys to your > database. You can add decoys using the tool in the TPP, or you can > simply embed your proteins of interest in a database for another > organism whose proteins should not give you any positive hits. > > On Oct 21, 3:24 pm, James Broadbent <[email protected]> wrote: >> Thanks Kristian. I think my concept of databases and specifying >> taxonomy is a little underdeveloped. I think what I really want is a >> smaller, specific database. >> >> On Oct 22, 2:59 am, Kristian <[email protected]> wrote: >> >> > Do you mean search a specific database? The taxonomy file specifies >> > the location of a database. >> > The GUI automatically generates a taxonomy file based on the database >> > and location you specify. >> > If you're going to run things in command line, there are other things >> > you can do. >> >> > What are you trying to do? >> >> > To specify the taxonomy, modify the line >> > <note type="input" label="list path, taxonomy information">C:\Inetpub >> > \wwwroot\ISB\data\parameters\taxonomy.xml</note> >> > in your tandem.params file. >> >> > The line I have above is, I believe, the default location. >> >> > On Oct 20, 8:20 pm, James Broadbent <[email protected]> wrote: >> >> > > Hi Everyone! >> >> > > Can anyone tell me how to search a specific taxonomy by specifying it >> > > in the tandem.params file when running searches in the TPP GUI? >> >> > > Thanks, >> >> > > James > > -- > 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. > > -- 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.
