# extrinsic information configuration file for AUGUSTUS
# 
# include with --extrinsicCfgFile=filename
# date: 15.4.2015
# Mario Stanke (mario.stanke@uni-greifswald.de)


# source of extrinsic information:
# M manual anchor (required)
# P protein database hit
# E EST/cDNA database hit
# C combined est/protein database hit
# D Dialign
# R retroposed genes
# T transMapped refSeqs
# W wiggle track coverage info from RNA-Seq

[SOURCES]
M RM P E T W

#
# 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]
E 1group1gene
T 1group1gene

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

[GENERAL]
      start      1.5      0.8  M    1  1e+100   RM  1   1   P  1   1e3   E  1    1   T  1    1  W  1   1
       stop	 1.5      0.8  M    1  1e+100   RM  1   1   P  1   1e3   E  1    1   T  1    1  W  1   1
        tss	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
        tts	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
        ass	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
        dss	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
   exonpart      1  .992 .985  M    1  1e+100   RM  1   1   P  1     1   E  1  1e3   T  1  1.4  W  1   1.02
       exon	 1        0.9  M    1  1e+100   RM  1   1   P  1   1e4   E  1    1   T  1    1  W  1   1
 intronpart	 1          1  M    1  1e+100   RM  1   1   P  1   1e3   E  1  1e4   T  1  1.4  W  1   1
     intron	 1.15    .168  M    1  1e+100   RM  1   1   P  1    1    E  1 1e10   T  1   1e5 W  1   1
    CDSpart	 1.5   1 .985  M    1  1e+100   RM  1   1   P  1  1e20   E  1    1   T  1 1e20  W  1   1
        CDS	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
    UTRpart	 1     1 .985  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1 1e10  W  1   1
        UTR	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
     irpart	 1          1  M    1  1e+100   RM  1   1   P  1     1   E  1    1   T  1    1  W  1   1
nonexonpart	 1          1  M    1  1e+100   RM  1 1.15  P  1     1   E  1    1   T  1    1  W  1   1
  genicpart	 1          1  M    1  1e+100   RM  1   1   P  1   1.5   E  1    1   T  1    1  W  1   1
#
# Explanation: see original extrinsic.cfg file
#