CoryneRegNet7

In this repository one can find the source code of CoryneRegNet (https://www.exbio.wzw.tum.de/coryneregnet/).

Packages:

com.coryneregnet.controller

• These classes carry information between layers, they are mostly used to carry information and make any necessary processing in the data before handing it to the database access layer (dao).

com.coryneregnet.dao

• Database access layer, every communication between the database and the code occurs through these classes.

com.coryneregnet.model

• These classes map the tables in the database.

com.coryneregnet.processing

• In the processing layer, the regulatory and genomic data are processed and the TRN transference occurs.

  AlignBindingSites.java: this class align binding sites using clustalo.

  GetHmmLogo.java: this class gets the hmm logos using skyalign.

  HomologyDetection.java: this class detects homology using BLAST.

  OperonPrediction.java: this class predicts operons.

  PromoterRegionPrediction.java: this class gets the upstream regions.

  RunHmmer.java: this class runs hmmer.

  RunPipeline.java: this class runs the transfer pipeline.

  SearchBindingSites.java: this class implements the binding site search.

  TransferRegularoryNetwork.java: this class runs TRN transfer itself.

com.coryneregnet.processing.input

• These classes are responsible for processing every input into the database.

com.coryneregnet.processing.output

• These classes are responsible for processing every output file.

com.coryneregnet.processing.statistics

• All the statistics are calculated in these classes.

com.coryneregnet.test

• Test classes.

com.coryneregnet.validation

• Validation classes.