Disperse design examples

Example design - TP53

A small example is provided so that you can try Disperse out. The examples directory contains the following files:

  • example_genelist

    Contains a single gene entry 'TP53'.

  • example_master.snp

    A small SNP data file to enable testing the SNP functionality without installing the big SNP data file.

  • example_settings.txt

    An example settings file.

  • example_reactions.xml

    An example restriction reaction file.

  • example_vector.lib

    An example vector sequence file.

  • example.cfg

    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.

  • example_genelist.target

    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.

Full test

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.

Limited test - No SNP data file available

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

Limited test - No Blast installation available

perl ../scripts/disperse.pl -i example_genelist -s example_settings.txt -start 4

or combine with '-nosnp' as above.

Example design - Chromosome 18

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.

  • Allowing 3 reactions from a pool of 120 reactions (15 enzymes and all combinations of them)
  • Allowing 3 reactions from a set of 24 of those reactions (this set was randomly selected from the large set)
  • Allowing 6 reactions from the set of 24 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.