# Parameter file: GeneID in P.marinus # Comment lines must begin with '#' # Non_homologypenalty NO_SCORE 0 # Number of isochores number_of_isochores 1 # PARAMETERS FROM ISOCHORE 1 # %GC boundaries_of_isochore 0 100 # Exons score: cutoffs Absolute_cuttoff_exons -150 -150 -150 -150 Coding_cutoff_Oligos -100 -150 -150 -150 # Exon score: factors Site_factor 0.65 0.65 0.65 0.65 Exon_factor 0.35 0.35 0.35 0.35 HSP_factor 1.0 1.0 1.0 1.0 Exon_weigths -3.55 -3.525 -3.525 -3.55 # Parameters to Predict Sites: Lenght, Offset, Cutoff and order (Markov chain) Start_profile 10 5 -5 0 # These are the start transition probabilities Acceptor_profile 15 13 -7 0 # These are the acceptor transition probabilities Donor_Profile 7 1 -5 1 # These are the donor transition probabilities Stop_Profile 4 0 -9999 0 # These are the transition probabilities 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 # Parameters to Predict Exons: Markov chains(initial - transition) Markov_oligo_logs_file 5 Markov_Initial_probability_matrix Markov_Transition_probability_matrix # How many donors per acceptor can we use to build exons? maximum_number_of_donors_per_acceptor_site 5 # Global Parameters # GENE MODEL: Rules about gene assembling (GenAmic) General_Gene_Model # INTRAgenic connections First+:Internal+ Internal+:Terminal+ 15:2000 block Terminal-:Internal- First-:Internal- 15:2000 blockr # External features Promoter+ First+:Single+ 50:4000 Terminal+:Single+ aataaa+ 50:4000 First-:Single- Promoter- 50:4000 aataaa- Single-:Terminal- 50:4000 # INTERgeneic connections aataaa+:Terminal+:Single+ Single+:First+:Promoter+ 150:Infinity aataaa+:Terminal+:Single+ Single-:Terminal-:aataaa- 150:Infinity Promoter-:First-:Single- Single+:First+:Promoter+ 150:Infinity Promoter-:First-:Single- Single-:Terminal-:aataaa- 150: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