This package is based on activities of the OGMP (i.e, priori to 2002), and becomes open source as part of MFannot.

This repository contains all the data needed by MFannot to run. That's includes the following:

• The EGC directory contains all Genetic Code Table in EGC.* files.
• config directory contains:
  • .mfannot_external_programs.conf is used by MFAnnot to allow it to run external programs. HMMsearchWrapper and HMMCombiner is used to find rns and rnl. RNAfinder is used to find tRNAs, rnpB, rrn5, group I introns, and group II introns.
  • .motsearch.pat is used by MFannot to find specific element in genome.
• The models directory contain the following sub-directory:
  • Erpin_models contains all the *.epn files used by RNAfinder.
  • HMM_models contains all the *.hmm file used by MFannot, organized in different sub-directory:
    • RNA for rns and rnl models this one is used by HMMsearchWrapper and HMMCombiner.
    • id_by_gene it contains HMM models for gene, this method of identification is used by MFannot only if the identification by BLAST failed.
  • Splice contains 2 *.mod files used by MFannot in order to identify splice site of group I introns or splice site of group II introns. And a neutral.pssm used to define neutral splice site for exonerate.
• The protein_collections contains:
  • identified directory that contains *.faa used by MFannot to identified gene by BLAST.
  • intronic_orfs.pep contains a list of intronic orfs used by MFannot to identify them.
  • family.lib contains list of family.

In order to run MFannot you should to setup the following environment variable:

• EGC to point to MFannot_data/EGC.
• MFANNOT_HOME to point to the installation path.
• MFANNOT_EXT_CFG_PATH to point to MFannot_data/config.
• MFANNOT_MOD_PATH to point to MFannot_data/models.
• ERPIN_MOD_PATH to point to MFannot_data/models/Erpin_models.
• MFANNOT_LIB_PATH to point to MFannot_data/protein_collections.

Please see CONTRIBUTING and CONDUCT for details.

• All Contributors

GNU General Public License v3.0. Please see License File for more information.