# extrinsic information configuration file for AUGUSTUS
# include with --extrinsicCfgFile=filename
# date: 01.08.2006
# Mario Stanke (mario@soe.ucsc.edu)


# source of extrinsic information:
# M manual anchor (required)
# P protein database hit
# E est database hit
# C combined est/protein database hit
# D Dialign
# R retroposed genes
# T transMapped refSeqs
# PB PacBio (long reads, circular consensus)

[SOURCES]
M RM PB

#
# individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set
# and the whole hint group is disregarded when one hint in it is unsatisfiable.
# 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for
# hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.
#
[SOURCE-PARAMETERS]

#   feature        bonus         malus   gradelevelcolumns
#		r+/r-
#
# the gradelevel colums have the following format for each source
# sourcecharacter numscoreclasses boundary    ...  boundary    gradequot  ...  gradequot
# 

[GENERAL]
      start     1          1  M    1  1e+100  RM  1     1    PB    1       1
       stop     1          1  M    1  1e+100  RM  1     1    PB    1       1
        tss     1          1  M    1  1e+100  RM  1     1    PB    1       1
        tts     1          1  M    1  1e+100  RM  1     1    PB    1       1
        ass     1          1  M    1  1e+100  RM  1     1    PB    1       1
        dss     1          1  M    1  1e+100  RM  1     1    PB    1       1
   exonpart     1       0.98  M    1  1e+100  RM  1     1    PB    1       1e5
       exon     1          1  M    1  1e+100  RM  1     1    PB    1       1e10
 intronpart     1          1  M    1  1e+100  RM  1     1    PB    1       1  
     intron     1         .1  M    1  1e+100  RM  1     1    PB    1       1e10  
    CDSpart     1          1  M    1  1e+100  RM  1     1    PB    1       1
        CDS     1          1  M    1  1e+100  RM  1     1    PB    1       1
    UTRpart     1          1  M    1  1e+100  RM  1     1    PB    1       1
        UTR     1          1  M    1  1e+100  RM  1     1    PB    1       1
     irpart     1          1  M    1  1e+100  RM  1     1    PB    1       1
nonexonpart     1          1  M    1  1e+100  RM  1  1.15    PB    1       1
  genicpart     1          1  M    1  1e+100  RM  1     1    PB    1       1


#
# Explanation: see original extrinsic.cfg file
#
