A small example is provided so that you can try Disperse out. The examples directory contains the following files:
Contains a single gene entry 'TP53'.
A small SNP data file to enable testing the SNP functionality without installing the big SNP data file.
An example settings file.
An example restriction reaction file.
An example vector sequence file.
Example configuration file, specifying the example_master.snp file as SNP data file. Use this to test the SNP data functionality, and make sure to edit any other properties if needed.
An example target file for the TP53 design. This is what would be generated in stage 3 of the pipeline. So, if you don't have fastacmd and a Blast database installed, you can still test stage 4 and onwards.
This requires the SNP data file to be installed (or an empty file in its place), and a local install of fastacmd and Blast database.
From the examples directory, execute:
perl ../scripts/disperse.pl -i example_genelist -s example_settings.txt
On Windows, use instead of / in all examples.
This requires a local install of fastacmd and Blast database to be available.
From the examples directory, execute:
perl ../scripts/disperse.pl -i example_genelist -s example_settings.txt -nosnp
or
perl ../scripts/disperse.pl -i example_genelist -s example_settings.txt -c example.cfg
perl ../scripts/disperse.pl -i example_genelist -s example_settings.txt -start 4
or combine with '-nosnp' as above.
An example of a selector design for all CCDS-annotated genes on chromosome 18. This design was performed using three different settings as regards the number of reactions.
All other settings were the same for the three designs. The design result files can be found in the examples section on this web site.