Difference between revisions of "MStoolbox"
From Marcotte Lab
(→MS-GFDB) |
(→Tide) |
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== Tide == | == Tide == | ||
* http://noble.gs.washington.edu/proj/tide/ | * http://noble.gs.washington.edu/proj/tide/ | ||
+ | |||
+ | === DB setup === | ||
+ | $ /project/marcotte/ms/bin/tide-index --enzyme=trypsin --digestion=full-digest --mods_spec=C+57.02156 --fasta UPS_combined.fa | ||
== MS-GFDB == | == MS-GFDB == |
Revision as of 15:34, 27 June 2012
Contents |
Before you start
For using MSblender, you need to run multiple search engines.
Repository
Crux
Tide
DB setup
$ /project/marcotte/ms/bin/tide-index --enzyme=trypsin --digestion=full-digest --mods_spec=C+57.02156 --fasta UPS_combined.fa
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$