##Descripton

This program calculates the effects of nsSNPs (non-synonymous single nucleotide polymorphisms) in the protein-coding regions of the human genome on the resulting protein-protein interaction network (PPIN). It was written as part of my Bachelor Thesis at the Chair of Computational Biology, Saarland University.

Installation

Download the jar and json files from the binaries folder or clone and import into Eclipse. Java version 8 or newer is required.

Parameters

A general main method is provided in the class Main in the framework folder. The command line options are:

• -m <file>

  File containing RefSNP identifiers (rs#), one per line. Required parameter. Example files can be found in the exampledata folder. Files in the gzip (*.gz) format are supported.

• -o <file>

  Output file. If not specified, a file named results.txt is created.

• -p <file>

  File containing protein-protein interactions, one interaction per line, tab-separated, Uniprot AC format. Optional parameter, otherwise a consensus PPIN (IntAct + BioGRID) is used.

• -update_ppin

  Data on the default consensus PPIN is saved in protein_tmp.json. If this flag is activated, the data is updated. This can take several minutes. The option should also be activated if a user-specified PPIN is provided.

• -localmutations

  Data on the last set of evaluated mutations is saved locally to mutation_tmp.json. If the same set of mutations is evaluated twice or more in a row, this option can be activated to use the locally stored data instead of downloading it every time.

• -nologfile

  Prevents log.txt from being created.

• -printlog

  Print output of logging system to the console. Significantly slows down the program, read log.txt instead.

##API Reference

Otherwise, the MutationEvaluator class encompasses all the functions of the program. To change any settings, the Settings class should be used. The settings are:

• LOCAL_MUTATION_DATA

  Data on the last set of evaluated mutations is saved locally to mutation_tmp.json. If the same set of mutations is evaluated twice or more in a row, this option can be activated to use the locally stored data instead of downloading it every time. Default: false

• LOCAL_PROTEIN_DATA

  Data on the default consensus PPIN is saved in protein_tmp.json. If this flag is activated, the data is updated. This can take several minutes. The option should also be activated if a user-specified PPIN is provided. Default: true

• DOMAIN_DATA_3DID

  Include 3did data in the DDI database. Default: true

• DOMAIN_DATA_IPFAM

  Include iPfam data in the DDI database. Default: true

• DOMAIN_DATA_IDDI

  Include IDDI data in the DDI database. Default: true

• DOMAIN_DATA_DOMINE

  Include DOMINE data in the DDI database. Default: true

• DOMAIN_DATA_NO_PREDICTIONS

  Only use experiment-based data. Default: true

• DISABLE_LOG

  Prevent logging system from printing to console. Default: false

• DISABLE_LOG_FILE

  Prevent logging system from writing a file. Default: false

• CLASSIFIER_BLOSUM_MATRIX

  BlosumMatrixName enum type incdicating which matrix to use. Default: BlosumMatrixName.BLOSUM100

• BINDING_SITE_CLASSIFIER

  ClassifierScore enum type indicating which classifier to use. Default: ClassifierScore.POLYPHEN_2_HC

Tests

The evaluation can be run by executing the main method in the eval subfolder. The testing data can be recreated using the scripts in the scripts folder.