# extrinsic information configuration file for AUGUSTUS
# 
# protein hints
# include with --extrinsicCfgFile=filename
# date: 16.10.2007
# Mario Stanke (mstanke@gwdg.de)


# 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

[SOURCES]
M P

#
# 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     0.3  M    1  1e+100  P  1  1000
       stop        1     0.3  M    1  1e+100  P  1  1000
        tss        1       1  M    1  1e+100  P  1     1
        tts        1       1  M    1  1e+100  P  1     1
        ass        1     0.8  M    1  1e+100  P  1   300
        dss        1     0.8  M    1  1e+100  P  1   300
   exonpart        1       1  M    1  1e+100  P  1     1
       exon        1       1  M    1  1e+100  P  1     1
 intronpart        1       1  M    1  1e+100  P  1     1
     intron        1       1  M    1  1e+100  P  1     1
    CDSpart        1    .995  M    1  1e+100  P  1   100		
        CDS        1     0.3  M    1  1e+100  P  1   1e4
    UTRpart        1       1  M    1  1e+100  P  1     1
        UTR        1       1  M    1  1e+100  P  1     1
     irpart        1       1  M    1  1e+100  P  1     1
nonexonpart        1       1  M    1  1e+100  P  1     1
  genicpart        1       1  M    1  1e+100  P  1     1

#
# Explanation: see original extrinsic.cfg file
#