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Richard Durbin rd at sanger.ac.uk
Fri Mar 26 04:24:55 EST 1999

Hello Jody,

I don't know what NetPlantGene output looks like, but with the new version
of acedb (4_7, available from the ftp sites), it is possible to store splice
and gene prediction information from other sources and use it in the
interactive genefinder facility.

Splice information should be stored under the model section:

?Sequence ...
	  Splices	Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
			Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)

with the method controlling display features like width, min_score,
max_score, right_priority.  e.g. here is the GF_splice Method object
showing the default values for genefinder splicing:

Method : "GF_splice"
Score_bounds     -2.000000 4.000000
Width    10.000000
Right_priority   5.600000

There is then now a "Parameters" option in the Genefinder... menu that
lets you set all the assembly parameters and list which methods should
be used and how to scale them.  You can edit this window and save as
another type of method object.  The default one will be
"assembly-default", which looks like this for my test database:

Method : "assembly-default"
Colour   RED
Right_priority   2.000000
Gene_assemble_method     "GF_ATG" 1.000000
Gene_assemble_method     "GF_splice" 1.000000
Gene_assemble_method     "hexExon_span" 0.200000
Intron_min       40
Exon_min         33
Intron_cost      -3.000000 -1.500000 55
Inter_gene_cost  -5.000000
GF_range         10000
GF_ATG_cutoff    0.000000
GF_5_cutoff      -0.500000
GF_3_cutoff      0.000000

The corresponding model bits are:

?Method ...
	Gene_assemble	Gene_assemble_method ?Method UNIQUE Float
				// Float factor to multiply score by
			Intron_min UNIQUE Int
			Exon_min UNIQUE Int
			Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
				// base cost, cost per log bp beyond min
				// Int is min for this if not Intron_min
			Inter_gene_cost UNIQUE Float
		// preceding paragraph determines dynamic programming
		// gene assembly from Genefinder... menu
	GF_parameters	GF_range UNIQUE Int
				// +- range for genefinder feature calculation
			GF_ATG_cutoff UNIQUE Float
			GF_5_cutoff UNIQUE Float
			GF_3_cutoff UNIQUE Float
		// preceding paragraph controls internal feature calculation


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