RG::Modules

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RG::Liu

  • euclid.pm: Euclid functions by J. Tamames & A.Valencia
  • libBlast.pm: functions for parsing blast output
  • libChop.pm, libChopper.pm: functions for CHOP and CHOPnet
  • libDna.pm: DNA sequence related functions
  • libFile.pm: common functions for processing files
  • libGenome.pm: genome related functions
  • libHmmer.pm: parsing HMMER output
  • libHssp.pm: parsing HSSP files
  • libList.pm: processing perl lists
  • libNesg.pm: NESG related functions
  • libNors.pm: NORS related functions
  • libPDB.pm: PDB functions
  • libPHD.pm: parsing PHD/PROF files
  • libSeq.pm: processing protein sequence files
  • libSwiss.pm: SWISS-PROT related

TODO

libxml-dom-perl needs to be added as a dependency, required by libChopper.

Driver scripts

Drier scripts are installed in __PREFIX__/usr/share/librg-utils-perl/

RG::Dudek

  • blastpgp.pm - blastpgp wrapper runs four (4) iterations of blastpgp. the first is a search over the non-redundant set and the following three (3) iterations are run over the redundant databases with the first iteration check file as a starting point.
  • blastpgp.pl - client script to blastpgp.pm

Driver scripts

Drier scripts are installed in __PREFIX__/usr/share/librg-dudek-bundle-perl/


RG::Utils

  • hssp_filter.pm - Filtering an hssp profile
  • hssp_filter.pl - client script
  • copf.pm
  • copf.pl
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