#
# CDS Searching parameters
#

Notify "  using default exonerate parameters"

#
# general parameters 
# may be overriden by enviroment variables (AssignUndef)
#

AssignUndef TMP_CLEANUP 1

#
# pass1: exonerate speedup
#
AssignUndef PASS1_SPEEDUP   1
AssignUndef PASS1_SLOWDOWN  5

AssignUndef PASS1_BLASTX_FILTER_MINLEN 100
AssignUndef PASS1_BLASTX_FILTER_IDMIN   50
AssignUndef PASS1_BLASTX_FILTER_NBMIN   20
AssignUndef PASS1_BLASTX_FILTER_NBMAX   20
AssignUndef PASS1_BLASTX_FILTER_COMIN    0.8
AssignUndef PASS1_BLASTX_FILTER_GCODE   11

#
# pass1: exonerate parameters
#
AssignUndef PASS1_PERCENT       30
AssignUndef PASS1_MIN_INTRON    30
AssignUndef PASS1_MAX_INTRON    6000
AssignUndef PASS1_GENETIC_CODE  11
AssignUndef PASS1_BESTN         10
AssignUndef PASS1_FRAMESHIFT    -100

# pass1: exonerate use Blosum62 with larger penalty for Stops
AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat

# comment next lines to use default or specific splice model
# AssignUndef SPLICE3MODEL $ModelsDir/splice.none.frq
# AssignUndef SPLICE5MODEL $ModelsDir/splice.none.frq

#
# pass1: cluster selection parameters
#
AssignUndef PASS1_MAX_SPAN    10000
AssignUndef PASS1_ALLOW_STOP  0
AssignUndef PASS1_LOOK_FOR_PSEUDO 1

#
# extension parameters
#
AssignUndef PASS1_START_WALK  120
AssignUndef PASS1_STOP_WALK   -1