2015-11-08 14:28:05 +01:00
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#
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# CDS Searching parameters
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#
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#
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# general parameters
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# (may be overriden by enviroment variables)
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#
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AssignUndef TMP_CLEANUP 1
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#
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# pass1: exonerate speedup
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#
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2015-11-08 18:52:59 +01:00
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AssignUndef PASS1_SPEEDUP 0
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2015-11-08 14:28:05 +01:00
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AssignUndef PASS1_SLOWDOWN 0
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AssignUndef PASS1_BLASTX_FILTER_IDMIN 70
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AssignUndef PASS1_BLASTX_FILTER_NBMIN 50
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AssignUndef PASS1_BLASTX_FILTER_NBMAX 200
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#
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# pass1: exonerate parameters
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#
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AssignUndef PASS1_PERCENT 30
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AssignUndef PASS1_MIN_INTRON 30
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AssignUndef PASS1_MAX_INTRON 6000
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AssignUndef PASS1_GENETIC_CODE 11
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AssignUndef PASS1_BESTN 10
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AssignUndef PASS1_FRAMESHIFT -100
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# pass1: exonerate use Blosum62 with larger penalty for Stops
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AssignUndef PASS1_SUBMAT $MODELS_DIR/blosum62.mat
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# comment next lines to use default or specific splice model
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# AssignUndef SPLICE3MODEL $MODELS_DIR/splice.none.frq
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# AssignUndef SPLICE5MODEL $MODELS_DIR/splice.none.frq
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#
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# pass1: cluster selection parameters
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#
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AssignUndef PASS1_MAX_SPAN 10000
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AssignUndef PASS1_ALLOW_STOP 0
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#
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# extension parameters
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#
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AssignUndef PASS1_START_WALK 120
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AssignUndef PASS1_STOP_WALK -1
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