# 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 E W XNT

#
# 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]
XNT 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          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
       stop      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
        tss      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
        tts      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
        ass      1      1 0.1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
        dss      1      1 0.1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
   exonpart      1  .988 .975  M    1  1e+100  RM  1     1    E 1    1    W 1    1.03   XNT 1    1
       exon      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
 intronpart      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
     intron      1        .26  M    1  1e+100  RM  1     1    E 1 1e10    W 1    1      XNT 1  1e3
    CDSpart      1     1 .975  M    1  1e+100  RM  1     1    E 1    1	  W 1    1      XNT 1  1e4
        CDS      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
    UTRpart      1     1 .985  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
        UTR      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
     irpart      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1
nonexonpart      1          1  M    1  1e+100  RM  1     1.15 E 1    1    W 1    1      XNT 1    1
  genicpart      1          1  M    1  1e+100  RM  1     1    E 1    1    W 1    1      XNT 1    1

#
# Explanation: see original extrinsic.cfg file
#
