#
# extrinsic information
# date: 29.4.2009
# 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
# MS peptide mass spectrometry

[SOURCES]
M E MS


#
# 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

#   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  E    1       1        MS  1    1
       stop             1             1  M    1  1e+100  E    1       1        MS  1    1
        tss             1             1  M    1  1e+100  E    1       1e2      MS  1    1
        tts             1             1  M    1  1e+100  E    1       1e5      MS  1    1
        ass             1             1  M    1  1e+100  E    1       20       MS  1    1
        dss             1             1  M    1  1e+100  E    1       20       MS  1    1
   exonpart             1             1  M    1  1e+100  E    1       1e2      MS  1    1
       exon             1             1  M    1  1e+100  E    1       1e3      MS  1    1
 intronpart             1             1  M    1  1e+100  E    1       1        MS  1    1
     intron             1             1  M    1  1e+100  E    1       5e3      MS  1  1e4
    CDSpart             1             1  M    1  1e+100  E    1       1        MS  1  1e3 
        CDS             1             1  M    1  1e+100  E    1       1        MS  1    1
    UTRpart             1             1  M    1  1e+100  E    1       1        MS  1    1
        UTR             1             1  M    1  1e+100  E    1       1        MS  1    1
     irpart             1             1  M    1  1e+100  E    1       1        MS  1    1
nonexonpart             1             1  M    1  1e+100  E    1       1        MS  1    1
  genicpart             1             1  M    1  1e+100  E    1       1        MS  1    1


# Explanation: see original extrinsic.cfg file
#
