######################################################################
# SPA PARAMETER FILE
######################################################################

######## GENERAL REMARKS ###############################
# Spa uses a probabilistic Bayesian models to score alignments
# Dynamic programming is used to find the optimal alignment under this model
# To keep running times feasible we use the BLAT gfserver to identify genomic loci
# and only try to align those loci.
# In addition, for each locus, we first find regions of homology between clone and genome
# and only do the dynamic programming for a subset of positions in the dynamic programming matrix
# that are in or near such regions of homology. We call these 'defined positions' of the dynamic
# programming matrix.
# The parameters in this file control
# 1. the specifics of the Bayesian model (i.e. likelihoods of various gene structures and sequencing errors)
# 2. The heuristics that determine defined positions in the dynamic programming matrix (which trade-off running
#    time against alignment accuracy.

######################################################################
# Scoring Parameters

score_match 0.941151922723275
# for a mismatch to be introduced by sequencing error
# (or SNP)
# (if both defined, must sum to 1.0; if one defined, other will be
# set to make both to sum to 1.0)
score_match 0.941151922723275
score_mismatch 0.0588480772767247


# score_splice_NNNN - relative probability of various splice juctions
# (first two and last two bases of the intron GT-AG is the canonical boundary)
# (if all are defined, must sum to 1.0; otherwise sum must not exceed
# 1.0, and undefined terms will be set equal to each other so as to
# yield a total sum of 1.0)
score_splice_tttt  0.0000652644
score_splice_tttc  0.0001004066
# score_splice_ttta
score_splice_tttg  0.0001464264
# score_splice_ttct
# score_splice_ttcc
score_splice_ttca  0.0002292618
# score_splice_ttcg
# score_splice_ttat
# score_splice_ttac
score_splice_ttaa  0.0003296685
score_splice_ttag  0.0001506100
# score_splice_ttgt
# score_splice_ttgc
# score_splice_ttga
# score_splice_ttgg
score_splice_tctt  0.0000334689
# score_splice_tctc
# score_splice_tcta
# score_splice_tctg
# score_splice_tcct
# score_splice_tccc
# score_splice_tcca
# score_splice_tccg
# score_splice_tcat
# score_splice_tcac
# score_splice_tcaa
# score_splice_tcag
score_splice_tcgt  0.0000167344
# score_splice_tcgc
# score_splice_tcga
# score_splice_tcgg
score_splice_tatt  0.0000209180
score_splice_tatc  0.0000167344
score_splice_tata  0.0000995699
# score_splice_tatg
score_splice_tact  0.0000359791
score_splice_tacc  0.0000334689
# score_splice_taca
# score_splice_tacg
# score_splice_taat
# score_splice_taac
score_splice_taaa  0.0001188145
score_splice_taag  0.0000167344
# score_splice_tagt
score_splice_tagc  0.0000167344
# score_splice_taga
score_splice_tagg  0.0000334689
# score_splice_tgtt
# score_splice_tgtc
score_splice_tgta  0.0000610807
# score_splice_tgtg
# score_splice_tgct
score_splice_tgcc  0.0000644276
# score_splice_tgca
# score_splice_tgcg
# score_splice_tgat
# score_splice_tgac
# score_splice_tgaa
score_splice_tgag  0.0001422428
# score_splice_tggt
score_splice_tggc  0.0000209180
# score_splice_tgga
# score_splice_tggg
# score_splice_cttt
# score_splice_cttc
# score_splice_ctta
# score_splice_cttg
score_splice_ctct  0.0000167344
# score_splice_ctcc
# score_splice_ctca
# score_splice_ctcg
# score_splice_ctat
# score_splice_ctac
score_splice_ctaa  0.0000167344
# score_splice_ctag
# score_splice_ctgt
# score_splice_ctgc
# score_splice_ctga
# score_splice_ctgg
# score_splice_cctt
# score_splice_cctc
# score_splice_ccta
# score_splice_cctg
score_splice_ccct  0.0000393259
score_splice_cccc  0.0000502033
score_splice_ccca  0.0000217548
# score_splice_cccg
# score_splice_ccat
# score_splice_ccac
# score_splice_ccaa
# score_splice_ccag
# score_splice_ccgt
# score_splice_ccgc
# score_splice_ccga
# score_splice_ccgg
score_splice_catt  0.0000435095
score_splice_catc  0.0002844855
score_splice_cata  0.0001196513
# score_splice_catg
score_splice_cact  0.0000836722
score_splice_cacc  0.0003062402
# score_splice_caca
# score_splice_cacg
score_splice_caat  0.0000334689
score_splice_caac  0.0003681577
score_splice_caaa  0.0000334689
score_splice_caag  0.0002334455
# score_splice_cagt
score_splice_cagc  0.0000836722
score_splice_caga  0.0000284486
score_splice_cagg  0.0000903660
# score_splice_cgtt
score_splice_cgtc  0.0000443463
# score_splice_cgta
# score_splice_cgtg
score_splice_cgct  0.0000050203
# score_splice_cgcc
score_splice_cgca  0.0000167344
# score_splice_cgcg
# score_splice_cgat
# score_splice_cgac
score_splice_cgaa  0.0000167344
# score_splice_cgag
# score_splice_cggt
score_splice_cggc  0.0003012199
score_splice_cgga  0.0000209180
# score_splice_cggg
# score_splice_attt
# score_splice_attc
score_splice_atta  0.0000033469
# score_splice_attg
# score_splice_atct
# score_splice_atcc
# score_splice_atca
score_splice_atcg  0.0000334689
score_splice_atat  0.0000150610
score_splice_atac  0.0012216142
# score_splice_ataa
score_splice_atag  0.0001171410
# score_splice_atgt
# score_splice_atgc
# score_splice_atga
score_splice_atgg  0.0000167344
# score_splice_actt
# score_splice_actc
# score_splice_acta
score_splice_actg  0.0001004066
# score_splice_acct
# score_splice_accc
# score_splice_acca
score_splice_accg  0.0000150610
# score_splice_acat
# score_splice_acac
score_splice_acaa  0.0000669378
# score_splice_acag
# score_splice_acgt
# score_splice_acgc
# score_splice_acga
# score_splice_acgg
score_splice_aatt  0.0000184079
score_splice_aatc  0.0000359790
# score_splice_aata
score_splice_aatg  0.0000568971
# score_splice_aact
# score_splice_aacc
score_splice_aaca  0.0000058571
# score_splice_aacg
score_splice_aaat  0.0000100406
score_splice_aaac  0.0006359088
score_splice_aaaa  0.0009940258
score_splice_aaag  0.0003070770
# score_splice_aagt
# score_splice_aagc
# score_splice_aaga
score_splice_aagg  0.0000284486
# score_splice_agtt
# score_splice_agtc
# score_splice_agta
# score_splice_agtg
# score_splice_agct
# score_splice_agcc
score_splice_agca  0.0000209180
# score_splice_agcg
# score_splice_agat
# score_splice_agac
# score_splice_agaa
score_splice_agag  0.0000016734
# score_splice_aggt
# score_splice_aggc
# score_splice_agga
# score_splice_aggg
score_splice_gttt  0.0000167344
score_splice_gttc  0.0001171411
score_splice_gtta  0.0001598139
score_splice_gttg  0.0001338755
# score_splice_gtct
# score_splice_gtcc
# score_splice_gtca
# score_splice_gtcg
score_splice_gtat  0.0000669378
# score_splice_gtac
score_splice_gtaa  0.0001246716
score_splice_gtag  0.9832655588
# score_splice_gtgt
score_splice_gtgc  0.0000502033
# score_splice_gtga
# score_splice_gtgg
# score_splice_gctt
# score_splice_gctc
score_splice_gcta  0.0000334689
# score_splice_gctg
score_splice_gcct  0.0002116907
# score_splice_gccc
# score_splice_gcca
# score_splice_gccg
score_splice_gcat  0.0000016734
score_splice_gcac  0.0000334689
# score_splice_gcaa
score_splice_gcag  0.0068945898
score_splice_gcgt  0.0000167344
score_splice_gcgc  0.0000669378
score_splice_gcga  0.0000167344
# score_splice_gcgg
# score_splice_gatt
score_splice_gatc  0.0000937129
# score_splice_gata
score_splice_gatg  0.0000301220
score_splice_gact  0.0000167344
# score_splice_gacc
score_splice_gaca  0.0001480998
# score_splice_gacg
# score_splice_gaat
# score_splice_gaac
# score_splice_gaaa
# score_splice_gaag
score_splice_gagt  0.0000711214
# score_splice_gagc
# score_splice_gaga
score_splice_gagg  0.0000200813
# score_splice_ggtt
score_splice_ggtc  0.0000502033
# score_splice_ggta
# score_splice_ggtg
# score_splice_ggct
score_splice_ggcc  0.0000368158
score_splice_ggca  0.0001012433
score_splice_ggcg  0.0000242649
# score_splice_ggat
score_splice_ggac  0.0001263450
score_splice_ggaa  0.0000167344
# score_splice_ggag
score_splice_gggt  0.0001196512
score_splice_gggc  0.0001004066
score_splice_ggga  0.0001137942
# score_splice_gggg



# This parameter defines misorientation
min_diff_misorientation -3.10274537267395

# genome non-intron jump scoring curve parameters
# (specified as log(probability))
#These parameters control the probability of sequencing errors leading
#to deletions (from the clone) of various lengths.

score_genome_jump_beta0 -0.000394377619758212
score_genome_jump_beta1 -8.0213843175762
score_genome_jump_beta2 -2.43226999883175
score_genome_jump_beta3 -0.955301823393716
score_genome_jump_alpha -0.192709673430941


# clone non-intron jump scoring curve parameters
# (specified as log(probability))
#These parameters control the probability of sequencing errors leading
#to insertions (into the clone) of various lengths.
score_clone_jump_beta0 -0.000422229838654428
score_clone_jump_beta1 -8.17876484520891
score_clone_jump_beta2 -2.31658499607766
score_clone_jump_beta3 -0.638907411622949
score_clone_jump_alpha -0.109464704528563


# Intron parameters

# score_genome_extension - added to non intron genome jump
# = log of probability to NOT start an intron (controls exon-length distribution)
score_genome_extension -0.00189465384541848


shortest_intron_length 32
longest_intron_length 301284

score_intron -17.0270348262384
score_intron -17.0270348262384
score_intron -17.3147168986902
score_intron -16.1107440943642
score_intron -15.117492321354
score_intron -12.8430781053266
score_intron -11.0148489563172
score_intron -10.069347178508
score_intron -9.95830931637333
score_intron -10.5500624633487
score_intron -11.1616296569162
score_intron -11.954095648806
score_intron -12.3124498542644
score_intron -12.7170749791229
score_intron -12.7469024992458
score_intron -12.6588535983866
score_intron -12.9875785293217
score_intron -13.2442666566675
score_intron -13.2636010710189
score_intron -13.2983338779378
score_intron -13.332701521442
score_intron -13.387515551663
score_intron -13.2425461939624
score_intron -13.2927723662766
score_intron -13.4193536385032
score_intron -13.676078661013
score_intron -13.7949137746202
score_intron -14.0288056724858
score_intron -14.0531299557289
score_intron -14.1588992097891
score_intron -14.0978944626338
score_intron -14.1117814019655
score_intron -14.5068534545295
score_intron -14.5242599226195
score_intron -14.5869787426157
score_intron -14.7301108886791
score_intron -14.9661466924543
score_intron -15.1583143158742
score_intron -15.6077539661222
score_intron -15.177268537736
score_intron -15.5349336205088
score_intron -15.4940580798988
score_intron -15.7086745752572
score_intron -15.4849300338729
score_intron -15.8669697583566
score_intron -16.0665728760511
score_intron -16.2319152160487
score_intron -16.5771179555594
score_intron -16.592582181257
score_intron -16.7914687549256
score_intron -16.5544834249139
score_intron -16.8001806955276
score_intron -16.9013733030099
score_intron -17.3557969244336
score_intron -17.5492242086547
score_intron -17.193503327937
score_intron -17.8453451497523
score_intron -18.1807878735853
score_intron -18.2458227163495
score_intron -17.9709854488647
score_intron -18.3349191331086
score_intron -18.1312431004106
score_intron -18.786048302496
score_intron -18.608637939679
score_intron -19.0952276553824
score_intron -19.09619878516
score_intron -19.28447176354
score_intron -19.4982777280077
score_intron -19.6855102417107
score_intron -19.819884733618
score_intron -20.1704030985984
score_intron -20.0760395664013
score_intron -20.596499479308
score_intron -20.8790470564954
score_intron -21.1016300930755
score_intron -20.9622782034734
score_intron -21.1893212027298
score_intron -21.6246552165852
score_intron -21.6907883363254
score_intron -21.944866600154
score_intron -21.6308969675665
score_intron -21.8040701999861
score_intron -22.5268225684191
score_intron -23.1982382327675
score_intron -23.5307784857403
score_intron -23.3811563889627
score_intron -23.7139167024409
score_intron -24.1237562047331
score_intron -24.6853253028892
score_intron -26.3862548677859
score_intron -25.3791437088802
score_intron -26.5692655253307
score_intron -25.5621115934198
score_intron -26.7522725213506
score_intron -25.457434798685
score_intron -26.9352445451098
score_intron -27.0267412365151
score_intron -26.4251264320413
score_intron -27.2097689724052
score_intron -27.839775068297




######################################################################
# end SPA PARAMETER FILE
