Difference between revisions of "MStoolbox"
From Marcotte Lab
(→X!Tandem) |
(→MS-GFDB) |
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== MS-GFDB == | == MS-GFDB == | ||
* http://proteomics.ucsd.edu/Software/MSGFDB.html | * http://proteomics.ucsd.edu/Software/MSGFDB.html | ||
+ | |||
+ | === DB setup === | ||
+ | Using target only database. | ||
+ | $ java -cp /project/marcotte/ms/bin/MSGFDB.jar msdbsearch.BuildSA -tda 2 -d UPS_target.fa | ||
== X!Tandem == | == X!Tandem == |
Revision as of 15:30, 27 June 2012
Contents |
Before you start
For using MSblender, you need to run multiple search engines.
Repository
Crux
Tide
MS-GFDB
DB setup
Using target only database.
$ java -cp /project/marcotte/ms/bin/MSGFDB.jar msdbsearch.BuildSA -tda 2 -d UPS_target.fa
X!Tandem
DB setup
- Setup database with the following command. You need to make 'combined' database (FASTA file) before this.
$ /project/marcotte/ms/bin/fasta_pro.exe <your fasta file>
Here is an example.
$ /project/marcotte/ms/bin/fasta_pro.exe UPS_combined.fa fasta_pro file conversion utility, v. 2006.09.15 input path = UPS_combined.fa output path = UPS_combined.fa.pro db type = plain taejoon@ada:~/project/ups2/DB$