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diff orthologs/ucsb_hamster/lib/wisecfg/pb.gf @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/pb.gf	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,387 @@
+# Splice sites and intron regions information for GeneWise-21 May 1500
+# Created by Mor Amitai (mor@compugen.co.il)
+# dataset : ~/ftp/pub/PomBase/temp/cds_cdna ~/ftp/pub/PomBase/temp/cds_ex
+# Consensi are read from top down. The value, for a sequence,
+# is the number in the line of the first consensus that
+# matches the sequence.
+# Note: the set of sequences that are represented by a consensus
+# are all the sequences that match this consensus and none of the
+# previous consensi
+#
+# the numbers in types 5SS, 3SS, CDS, and the emissions are the number of
+# occurrences of each sequence in the database. 
+# In case of a consensus this is the number of occurrences of sequences 
+# that are represented by the consensus in the database divided by the 
+# number of sequences that are represented by the consensus.
+# *stay_prob is the probability of the transition from the state to itself.
+# No_Spacer_Prob is the probability of transition from Pyrimidine directly 
+# to 3SS (no spacer).
+type 5SS
+center 3
+phase all
+begin consensus
+---GTA-GT- 8.69141
+---GT----- 0.0821553
+end consensus
+type 5SS
+center 3
+phase 0
+begin consensus
+---GTA-GT- 3.71094
+---GT----- 0.0356523
+end consensus
+type 5SS
+center 3
+phase 1
+begin consensus
+---GTA-GT- 2.92969
+---GT----- 0.0294519
+end consensus
+type 5SS
+center 3
+phase 2
+begin consensus
+---GT----- 0.0488281
+end consensus
+type 3SS
+center 3
+phase all
+begin consensus
+TAG--- 1.64062
+-AG--- 22.9167
+end consensus
+type 3SS
+center 3
+phase 0
+begin consensus
+TAG--- 0.765625
+-AG--- 9.375
+end consensus
+type 3SS
+center 3
+phase 1
+begin consensus
+TAG--- 0.515625
+-AG--- 8.85417
+end consensus
+type 3SS
+center 3
+phase 2
+begin consensus
+-AG--- 12.5
+end consensus
+type CDS
+phase all
+begin consensus
+AAA 238.6335
+AAC 105.316
+AAG 156.4912
+AAT 168.6987
+ACA 98.7639
+ACC 64.5552
+ACG 58.8997
+ACT 105.1091
+AGA 126.4206
+AGC 83.1769
+AGG 72.7625
+AGT 86.5564
+ATA 99.3847
+ATC 104.0746
+ATG 139.4558
+ATT 185.1134
+CAA 149.8701
+CAC 57.5203
+CAG 70.8314
+CAT 95.1086
+CCA 79.5215
+CCC 49.1751
+CCG 45.5887
+CCT 83.2459
+CGA 70.6935
+CGC 36.8985
+CGG 35.4502
+CGT 74.1419
+CTA 83.6597
+CTC 86.1426
+CTG 91.798
+CTT 143.6629
+GAA 168.216
+GAC 64.1414
+GAG 82.3493
+GAT 125.593
+GCA 79.3146
+GCC 51.589
+GCG 36.4847
+GCT 96.488
+GGA 94.6258
+GGC 47.037
+GGG 35.2433
+GGT 84.6942
+GTA 73.7281
+GTC 68.8313
+GTG 72.4867
+GTT 127.5931
+TAA 113.0406
+TAC 99.9364
+TAG 59.1066
+TAT 138.5592
+TCA 115.9373
+TCC 92.1429
+TCG 76.4179
+TCT 120.5582
+TGA 148.7666
+TGC 96.7638
+TGG 118.0064
+TGT 96.6949
+TTA 153.8704
+TTC 145.5251
+TTG 156.6981
+TTT 212.8391
+end consensus
+type CDS
+phase 0
+begin consensus
+AAA 248.8005
+AAC 103.9424
+AAG 172.7552
+AAT 217.5971
+ACA 87.4108
+ACC 69.0194
+ACG 38.6426
+ACT 163.0428
+AGA 70.2593
+AGC 51.4546
+AGG 27.6904
+AGT 88.0307
+ATA 74.1855
+ATC 72.1191
+ATG 126.4667
+ATT 251.6935
+CAA 170.2754
+CAC 39.4692
+CAG 70.2593
+CAT 104.5623
+CCA 77.4918
+CCC 56.6207
+CCG 25.8306
+CCT 144.4448
+CGA 48.1483
+CGC 42.1556
+CGG 17.1515
+CGT 131.8395
+CTA 50.628
+CTC 47.735
+CTG 34.3031
+CTT 165.7292
+GAA 288.4763
+GAC 103.9424
+GAG 150.4375
+GAT 257.6862
+GCA 100.4294
+GCC 74.5988
+GCG 29.1369
+GCT 190.5266
+GGA 104.9756
+GGC 59.927
+GGG 26.4506
+GGT 158.29
+GTA 76.252
+GTC 75.0121
+GTG 49.5948
+GTT 200.6522
+TAA 0
+TAC 77.0786
+TAG 0
+TAT 147.7511
+TCA 102.4959
+TCC 77.2852
+TCG 41.5356
+TCT 182.6741
+TGA 0
+TGC 32.2366
+TGG 58.8938
+TGT 48.5616
+TTA 163.0428
+TTC 90.7171
+TTG 145.0647
+TTT 196.5193
+end consensus
+type CDS
+phase 1
+begin consensus
+AAA 234.9249
+AAC 117.7724
+AAG 221.908
+AAT 133.0621
+ACA 116.7393
+ACC 50.4148
+ACG 81.6142
+ACT 75.6223
+AGA 108.6812
+AGC 97.937
+AGG 113.4334
+AGT 73.5561
+ATA 169.427
+ATC 136.5747
+ATG 253.9338
+ATT 167.5674
+CAA 120.0452
+CAC 66.7377
+CAG 102.8959
+CAT 78.1017
+CCA 99.7966
+CCC 45.6626
+CCG 72.7296
+CCT 59.5061
+CGA 43.5964
+CGC 22.728
+CGG 37.8111
+CGT 30.9927
+CTA 166.1211
+CTC 141.3269
+CTG 215.7094
+CTT 157.6497
+GAA 86.573
+GAC 38.431
+GAG 54.5472
+GAT 44.0097
+GCA 61.5722
+GCC 35.5383
+GCG 47.5222
+GCT 41.117
+GGA 40.7038
+GGC 24.5876
+GGG 33.4722
+GGT 31.406
+GTA 107.6481
+GTC 79.1348
+GTG 150.4181
+GTT 89.4657
+TAA 114.0533
+TAC 76.862
+TAG 96.4907
+TAT 76.6554
+TCA 89.6723
+TCC 59.5061
+TCG 76.0355
+TCT 60.3325
+TGA 103.7224
+TGC 66.5311
+TGG 120.8717
+TGT 64.0517
+TTA 199.3866
+TTC 168.6005
+TTG 265.2978
+TTT 181.2042
+end consensus
+type CDS
+phase 2
+begin consensus
+AAA 231.6265
+AAC 94.221
+AAG 74.5916
+AAT 155.1753
+ACA 92.1547
+ACC 74.385
+ACG 56.6152
+ACT 76.6578
+AGA 200.2195
+AGC 100.2131
+AGG 77.2777
+AGT 98.1468
+ATA 54.549
+ATC 103.5191
+ATG 37.8124
+ATT 135.7526
+CAA 159.1012
+CAC 66.5332
+CAG 39.4654
+CAT 102.6926
+CCA 61.3676
+CCC 45.4575
+CCG 38.4322
+CCT 45.8707
+CGA 120.4623
+CGC 46.0774
+CGG 51.6562
+CGT 59.7146
+CTA 34.2997
+CTC 69.426
+CTG 25.4149
+CTT 107.445
+GAA 129.3472
+GAC 50.2099
+GAG 42.1515
+GAT 75.0048
+GCA 76.038
+GCC 44.8376
+GCG 33.06
+GCT 57.855
+GGA 138.2321
+GGC 56.8219
+GGG 46.0774
+GGT 64.467
+GTA 37.3991
+GTC 52.4827
+GTG 17.5631
+GTT 92.568
+TAA 224.8079
+TAC 145.8772
+TAG 80.7903
+TAT 191.128
+TCA 155.5886
+TCC 139.6784
+TCG 111.7841
+TCT 118.6027
+TGA 342.1709
+TGC 191.5413
+TGG 174.1848
+TGT 177.4908
+TTA 98.9733
+TTC 177.0775
+TTG 59.508
+TTT 260.3474
+end consensus
+type Intron_Corr_Term
+phase all
+ 225.12
+type Intron_Corr_Term
+phase 0
+ 524.049
+type Intron_Corr_Term
+phase 1
+ 652.388
+type Intron_Corr_Term
+phase 2
+ 998.969
+type Intron_emission
+begin consensus
+A 123.3115
+C 59.5593
+G 67.0399
+T 150.0893
+end consensus
+type Pyrimidine_emission
+begin consensus
+A 26.1549
+C 86.9936
+G 12.7932
+T 274.0583
+end consensus
+type Spacer_emission
+begin consensus
+A 149.5231
+C 60.7484
+G 51.3573
+T 138.3712
+end consensus
+type Intron_Stay_Prob
+ 0.988929
+type Central_Intron_Stay_Prob
+ 0.983466
+type Pyrimidine_Stay_Prob
+ 0.904578
+type No_Spacer_Prob
+ 0.0743243
+type Spacer_Stay_Prob
+ 0.952081