Eric Coissac
2ff6ff3308
PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time (Pseudogene search). The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO is set to 1 Former-commit-id: 318327af6bdc3fbdfbe7f438ff7cbea22863a0ab Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
56 lines
1.2 KiB
Plaintext
56 lines
1.2 KiB
Plaintext
#
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# CDS Searching parameters
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#
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Notify " using default exonerate parameters"
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#
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# general parameters
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# may be overriden by enviroment variables (AssignUndef)
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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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AssignUndef PASS1_SPEEDUP 1
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AssignUndef PASS1_SLOWDOWN 0
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AssignUndef PASS1_BLASTX_FILTER_IDMIN 80
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AssignUndef PASS1_BLASTX_FILTER_NBMIN 20
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AssignUndef PASS1_BLASTX_FILTER_NBMAX 50
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AssignUndef PASS1_BLASTX_FILTER_COMIN 0.8
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AssignUndef PASS1_BLASTX_FILTER_GCODE 11
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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 $ModelsDir/blosum62.mat
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# comment next lines to use default or specific splice model
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# AssignUndef SPLICE3MODEL $ModelsDir/splice.none.frq
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# AssignUndef SPLICE5MODEL $ModelsDir/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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AssignUndef PASS1_LOOK_FOR_PSEUDO 1
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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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