geneid_template.param

# geneid parameter file: S.lycopersicum
# Comment lines must begin with '#'

# Non-homology penalty
NO_SCORE
0

# Number of isochores
number_of_isochores
1

# PARAMETERS FROM ISOCHORE 1

# %GC
boundaries_of_isochore
0  100

# Exons score: cutoffs
Absolute_cutoff_exons
-150 -150 -150 -150

Coding_cutoff_oligos
-100 -150 -150 -150

# Exon score: factors
Site_factor
0.60 0.60 0.60 0.60

Exon_factor
0.5 0.5 0.5 0.5

HSP_factor
1.0 1.0 1.0 1.0

Exon_weigths
-4.0 -4.0 -4.0 -4.0

# Site prediction: Position Weight Arrays
# Lenght, Offset, Cutoff and order (Markov model)
Start_profile 

Acceptor_profile

Donor_profile

Stop_profile
4 0 -9999 0
# Transition stop probabilities at every position
1 A 0
1 C 0
1 G 0
1 T 0
2 A -9999
2 C -9999
2 G -9999
2 T 0.000
3 A 0.000
3 C -9999
3 G 0.000
3 T -9999
4 A 0.000
4 C -9999
4 G 0.000
4 T -9999


# Exon prediction: Markov model
Markov_oligo_logs_file

# Donors per acceptor to build exons
maximum_number_of_donors_per_acceptor_site
5

# GENE MODEL: Rules about gene assembling (GenAmic)
General_Gene_Model
# INTRAgenic connections
First+:Internal+                Internal+:Terminal+             25:7000 block
Terminal-:Internal-             First-:Internal-                25:7000 blockr
# External features
Promoter+                       First+:Single+                  50:4000
Terminal+:Single+               aataaa+                         50:4000
First-:Single-                  Promoter-                       50:4000
aataaa-                         Single-:Terminal-               50:4000
# INTERgenic conections
aataaa+:Terminal+:Single+       Single+:First+:Promoter+        700:Infinity
aataaa+:Terminal+:Single+       Single-:Terminal-:aataaa-       700:Infinity
Promoter-:First-:Single-        Single+:First+:Promoter+        700:Infinity
Promoter-:First-:Single-        Single-:Terminal-:aataaa-       700:Infinity
# BEGINNING and END of prediction
Begin+                          First+:Internal+:Terminal+:Single+ 0:Infinity
Begin-                          First-:Internal-:Terminal-:Single- 0:Infinity
First+:Internal+:Terminal+:Single+               End+              0:Infinity
First-:Internal-:Terminal-:Single-               End-              0:Infinity