#
# CDS Searching parameters
#

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

AssignUndef TMP_CLEANUP 1

#
# pass1: exonerate speedup
#
AssignUndef PASS1_SPEEDUP   0
AssignUndef PASS1_SLOWDOWN  0

AssignUndef PASS1_BLASTX_FILTER_IDMIN 70
AssignUndef PASS1_BLASTX_FILTER_NBMIN 50
AssignUndef PASS1_BLASTX_FILTER_NBMAX 200

#
# 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 $MODELS_DIR/blosum62.mat

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

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

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