######################################################################
# 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/score_mismatch - probability per base
# 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 0.997405881101064
score_mismatch 0.00259411889893624


# 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  0.0000723941
score_splice_tttc  0.0001690919
# score_splice_ttta
# score_splice_tttg
# score_splice_ttct
score_splice_ttcc  0.0003454231
score_splice_ttca  0.0002032205
# score_splice_ttcg
# score_splice_ttat
# score_splice_ttac
score_splice_ttaa  0.0000103420
score_splice_ttag  0.0001721945
# score_splice_ttgt
# score_splice_ttgc
# score_splice_ttga
score_splice_ttgg  0.0000351628
# score_splice_tctt
score_splice_tctc  0.0001752971
# score_splice_tcta
# score_splice_tctg
# score_splice_tcct
score_splice_tccc  0.0002937131
score_splice_tcca  0.0000589494
score_splice_tccg  0.0000206840
# score_splice_tcat
score_splice_tcac  0.0000103420
# score_splice_tcaa
# score_splice_tcag
score_splice_tcgt  0.0000206840
score_splice_tcgc  0.0000749796
# score_splice_tcga
# score_splice_tcgg
# score_splice_tatt
score_splice_tatc  0.0000517101
# score_splice_tata
score_splice_tatg  0.0000031026
# score_splice_tact
# score_splice_tacc
# score_splice_taca
# score_splice_tacg
# score_splice_taat
# score_splice_taac
score_splice_taaa  0.0000294747
# score_splice_taag
# score_splice_tagt
# score_splice_tagc
# score_splice_taga
# score_splice_tagg
# score_splice_tgtt
score_splice_tgtc  0.0003878254
# score_splice_tgta
score_splice_tgtg  0.0000439535
# score_splice_tgct
score_splice_tgcc  0.0014370223
score_splice_tgca  0.0001432369
# score_splice_tgcg
score_splice_tgat  0.0000434364
# score_splice_tgac
score_splice_tgaa  0.0000155130
# score_splice_tgag
score_splice_tggt  0.0000155130
score_splice_tggc  0.0010910821
score_splice_tgga  0.0000134446
score_splice_tggg  0.0000227524
# score_splice_cttt
score_splice_cttc  0.0000460219
score_splice_ctta  0.0000056881
score_splice_cttg  0.0000480904
# score_splice_ctct
score_splice_ctcc  0.0000434364
score_splice_ctca  0.0004715957
score_splice_ctcg  0.0000031026
# score_splice_ctat
# score_splice_ctac
# score_splice_ctaa
score_splice_ctag  0.0001184160
# score_splice_ctgt
score_splice_ctgc  0.0000444706
score_splice_ctga  0.0000475732
score_splice_ctgg  0.0001127279
# score_splice_cctt
# score_splice_cctc
# score_splice_ccta
# score_splice_cctg
score_splice_ccct  0.0000594666
score_splice_cccc  0.0008299463
score_splice_ccca  0.0001132450
# score_splice_cccg
# score_splice_ccat
# score_splice_ccac
# score_splice_ccaa
score_splice_ccag  0.0000718770
# score_splice_ccgt
# score_splice_ccgc
# score_splice_ccga
score_splice_ccgg  0.0000237866
score_splice_catt  0.0000103420
score_splice_catc  0.0000279234
# score_splice_cata
score_splice_catg  0.0000062052
score_splice_cact  0.0006841240
score_splice_cacc  0.0000760138
score_splice_caca  0.0001416856
# score_splice_cacg
# score_splice_caat
# score_splice_caac
score_splice_caaa  0.0000046539
score_splice_caag  0.0000765309
# score_splice_cagt
score_splice_cagc  0.0000387825
# score_splice_caga
score_splice_cagg  0.0000103420
# score_splice_cgtt
# score_splice_cgtc
# score_splice_cgta
# score_splice_cgtg
# score_splice_cgct
# score_splice_cgcc
# score_splice_cgca
# score_splice_cgcg
# score_splice_cgat
# score_splice_cgac
score_splice_cgaa  0.0000103420
# score_splice_cgag
# score_splice_cggt
# score_splice_cggc
# score_splice_cgga
score_splice_cggg  0.0001225528
# score_splice_attt
score_splice_attc  0.0000382654
score_splice_atta  0.0000310260
score_splice_attg  0.0001246212
# score_splice_atct
# score_splice_atcc
# score_splice_atca
# score_splice_atcg
score_splice_atat  0.0001039372
score_splice_atac  0.0016640295
score_splice_ataa  0.0001173818
score_splice_atag  0.0005036559
score_splice_atgt  0.0000310260
# score_splice_atgc
# score_splice_atga
score_splice_atgg  0.0000770480
# score_splice_actt
# score_splice_actc
# score_splice_acta
score_splice_actg  0.0000775651
# score_splice_acct
score_splice_accc  0.0010590218
score_splice_acca  0.0000206840
# score_splice_accg
# score_splice_acat
# score_splice_acac
score_splice_acaa  0.0000155130
score_splice_acag  0.0000692915
# score_splice_acgt
# score_splice_acgc
# score_splice_acga
score_splice_acgg  0.0000785993
score_splice_aatt  0.0000527443
score_splice_aatc  0.0000930781
# score_splice_aata
score_splice_aatg  0.0001535789
score_splice_aact  0.0001297922
score_splice_aacc  0.0003149142
score_splice_aaca  0.0000005171
# score_splice_aacg
score_splice_aaat  0.0000108591
score_splice_aaac  0.0003480086
score_splice_aaaa  0.0009152679
score_splice_aaag  0.0005207202
# score_splice_aagt
score_splice_aagc  0.0002688923
# score_splice_aaga
score_splice_aagg  0.0002016692
# score_splice_agtt
score_splice_agtc  0.0000677402
# score_splice_agta
# score_splice_agtg
# score_splice_agct
score_splice_agcc  0.0025027665
score_splice_agca  0.0000175814
# score_splice_agcg
# score_splice_agat
score_splice_agac  0.0000811848
score_splice_agaa  0.0000134446
# score_splice_agag
# score_splice_aggt
score_splice_aggc  0.0013248115
# score_splice_agga
score_splice_aggg  0.0008237411
score_splice_gttt  0.0000310260
score_splice_gttc  0.0000310260
score_splice_gtta  0.0000206840
score_splice_gttg  0.0005305451
score_splice_gtct  0.0000398167
score_splice_gtcc  0.0000966978
# score_splice_gtca
# score_splice_gtcg
score_splice_gtat  0.0000548127
score_splice_gtac  0.0000563640
score_splice_gtaa  0.0001494420
score_splice_gtag  0.9655611058
# score_splice_gtgt
score_splice_gtgc  0.0000330944
score_splice_gtga  0.0000051710
score_splice_gtgg  0.0005377845
# score_splice_gctt
# score_splice_gctc
# score_splice_gcta
# score_splice_gctg
# score_splice_gcct
score_splice_gccc  0.0002394175
# score_splice_gcca
# score_splice_gccg
# score_splice_gcat
# score_splice_gcac
score_splice_gcaa  0.0000341286
score_splice_gcag  0.0106109025
score_splice_gcgt  0.0002120112
score_splice_gcgc  0.0000925610
# score_splice_gcga
score_splice_gcgg  0.0004085094
# score_splice_gatt
score_splice_gatc  0.0000806677
# score_splice_gata
# score_splice_gatg
# score_splice_gact
score_splice_gacc  0.0002125283
# score_splice_gaca
# score_splice_gacg
score_splice_gaat  0.0000232695
# score_splice_gaac
# score_splice_gaaa
score_splice_gaag  0.0000517101
# score_splice_gagt
score_splice_gagc  0.0000558469
score_splice_gaga  0.0000356799
# score_splice_gagg
score_splice_ggtt  0.0000098249
score_splice_ggtc  0.0000708428
score_splice_ggta  0.0000480904
score_splice_ggtg  0.0000113762
# score_splice_ggct
score_splice_ggcc  0.0001571986
score_splice_ggca  0.0000475732
score_splice_ggcg  0.0000118933
score_splice_ggat  0.0000103420
score_splice_ggac  0.0000785993
score_splice_ggaa  0.0000041368
score_splice_ggag  0.0000599836
score_splice_gggt  0.0001003175
score_splice_gggc  0.0000186156
score_splice_ggga  0.0000573982
score_splice_gggg  0.0000424022



# This parameter defines misorientation
min_diff_misorientation -4.02723483713635

# 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 -0.000121391146735977
score_genome_jump_beta1 -9.52514829895243
score_genome_jump_beta2 -1.37170761562802
score_genome_jump_beta3 -0.908127421234994
score_genome_jump_alpha -0.195623231577161


# 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 -0.000125723633212713
score_clone_jump_beta1 -9.62535843820537
score_clone_jump_beta2 -1.34752166080142
score_clone_jump_beta3 -0.848477801527052
score_clone_jump_alpha -0.127436262582692


# 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 -0.00201887667799172


shortest_intron_length 30
longest_intron_length 506083

score_intron -16.2495684501711
score_intron -16.8686076585773
score_intron -16.1754604780174
score_intron -15.5186809416283
score_intron -15.734904050098
score_intron -15.7699953699092
score_intron -15.3363593848344
score_intron -15.7418244929425
score_intron -15.7010024984223
score_intron -14.5240583664843
score_intron -13.2850887201212
score_intron -12.4238577654301
score_intron -12.4416247302448
score_intron -12.7476366212399
score_intron -12.938464112036
score_intron -13.1668247996275
score_intron -13.4028717557776
score_intron -13.5807389622222
score_intron -13.7405947743005
score_intron -13.6838797211417
score_intron -13.6105111205559
score_intron -13.7503417466084
score_intron -13.7003418345956
score_intron -13.8377840652121
score_intron -13.9844278709291
score_intron -13.9708739042401
score_intron -14.0587747631652
score_intron -14.1693259472951
score_intron -14.1993972907914
score_intron -14.1739355834213
score_intron -14.2099728170385
score_intron -14.2448770427991
score_intron -14.3027114210148
score_intron -14.3742591169289
score_intron -14.4055681399533
score_intron -14.4519092588159
score_intron -14.5082552563162
score_intron -14.4869751477254
score_intron -14.5274889015811
score_intron -14.6590372454188
score_intron -14.7340485919042
score_intron -14.8129152971092
score_intron -14.8969259216596
score_intron -15.0165202007481
score_intron -15.0829784767467
score_intron -15.2070169044901
score_intron -15.3382374730033
score_intron -15.4675654408229
score_intron -15.5390151111342
score_intron -15.6686372139203
score_intron -15.8038234002821
score_intron -15.9102786836961
score_intron -16.0845955317118
score_intron -16.2908402631651
score_intron -16.4377814533786
score_intron -16.5937200625784
score_intron -16.7569442525894
score_intron -16.9271739606276
score_intron -17.1334603394828
score_intron -17.2474558915856
score_intron -17.4355785008861
score_intron -17.5965331992865
score_intron -17.7990451631486
score_intron -17.965057784241
score_intron -18.1298030265973
score_intron -18.2756944520826
score_intron -18.5241680207702
score_intron -18.6634668937265
score_intron -18.8306850437357
score_intron -18.86999381054
score_intron -19.1641024573464
score_intron -19.4524396892017
score_intron -19.6222984149461
score_intron -19.6941286570104
score_intron -19.8435028716885
score_intron -20.111970486637
score_intron -20.287046846674
score_intron -20.6097300209037
score_intron -20.7347682099074
score_intron -21.0856867043933
score_intron -21.152470044464
score_intron -21.498345371159
score_intron -21.5892274214416
score_intron -21.7869766488768
score_intron -22.0443526462906
score_intron -22.3525150441961
score_intron -22.546194831622
score_intron -22.5269510147003
score_intron -23.2976311322858
score_intron -23.0093443380615
score_intron -23.3637256188048
score_intron -23.8079325039772
score_intron -23.9552812740656
score_intron -24.538102909585
score_intron -24.8177462216609
score_intron -24.9663916042874
score_intron -25.5232461012491
score_intron -25.109753058292
score_intron -26.2568989388521
score_intron -26.2298517781301

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