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diff orthologs/ucsb_hamster/lib/wisecfg/human.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
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/human.gf	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,541 @@
+# Splice sites and intron regions information for GeneWise-21
+# Wed Jan  1 13:42:23 IST 1997
+# Created by Mor Amitai (mor@compugen.co.il)
+# dataset : hum1 and hum2 from embl48
+# 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
+C-GGTGAGTG 15.75
+--GGTGAGTG 8.83333
+CAGGTGAG-- 7.6
+AAGGTGAG-- 6.86667
+CAGGTAAG-- 4.3125
+GAGGTGAG-- 4.26667
+AAGGTAAG-- 4.1875
+--GGTGAGT- 1.71795
+---GTGAGTG 1.66667
+--GGTGAG-C 1.51282
+-A-GTAAGT- 1.41071
+-AGGTG-GT- 1.39583
+-TGGTAAG-- 1.39062
+CAGGTA-G-- 1.35417
+AAGGTA-G-- 1.04167
+-GGGTAAG-- 1
+--GGTGAG-- 0.91453
+-C-GTAAGT- 0.828125
+---GTGAGT- 0.729167
+-AGGTAA--- 0.578704
+-AGGTG-G-- 0.506944
+CAGGTA---- 0.381944
+--GGTA-GT- 0.339286
+-AGGTGA--- 0.265625
+--GGTCAG-- 0.207031
+---GTAAG-- 0.155556
+-AGGTA---- 0.134921
+-AGGT--G-- 0.111607
+--GGT--G-- 0.0369898
+-AGGT----- 0.0250947
+--GGTA---- 0.0234375
+--AGT--G-- 0.0132415
+---GT----- 0.00148067
+end consensus
+type 5SS
+center 3
+phase 0
+begin consensus
+A-GGTGAGTG 8.25
+C-GGTGAGTG 7.75
+AAGGTGAG-- 3.86667
+CAGGTGAG-- 3.46667
+AAGGTAAG-- 2.5
+GAGGTGAG-- 2.4375
+--GGTGAGT- 1.19565
+-AGGTAAG-- 1.02083
+-A-GTGAGT- 0.916667
+-AGGT--GTG 0.785714
+AAGGT-GG-- 0.716667
+-C-GTGAGT- 0.666667
+---GTAAGTG 0.566667
+--GGTGAG-- 0.423077
+--GGTAAG-- 0.355556
+CAGGT--G-- 0.3
+---GTAAGT- 0.284722
+-AGGTAA--- 0.265625
+--GGTA-GT- 0.196429
+-AGGTAC--- 0.157895
+AAGGTG---- 0.13964
+-AGGTG---- 0.048048
+-AGGT----- 0.0181818
+--GGT--G-- 0.0129717
+---GTA---- 0.00291667
+---GT----- 0.000915751
+end consensus
+type 5SS
+center 3
+phase 1
+begin consensus
+--GGTGAGTG 4.375
+CAGGTGAG-- 2.8
+AAGGTGAG-- 2.26667
+-AGGTAAG-- 1.01562
+-TGGTAAG-- 0.8125
+-TGGTGAG-- 0.7
+G-GGTGAG-- 0.755556
+CAGGT-GG-- 0.546875
+--GGTGAG-- 0.428571
+---GTGAGTG 0.625
+---GTAAGT- 0.223214
+AAGGT--G-- 0.200893
+-AGGTAA--- 0.1875
+--GGTA-G-G 0.175
+CAGGT----- 0.0733945
+---GTGAG-- 0.0527778
+--GGT--GT- 0.0512129
+A-GGTA---- 0.046398
+-AGGT----- 0.0137104
+---G-AAG-- 0.00972447
+---GT----- 0.00111909
+end consensus
+type 5SS
+center 3
+phase 2
+begin consensus
+-AGGTGAG-- 0.703125
+C--GTGAGT- 0.516667
+-AGGTAAG-- 0.5
+---GTAAGT- 0.241667
+--GGTGAG-- 0.227778
+CAGGTA---- 0.133333
+---GTGAG-- 0.0569444
+-AGGT--G-- 0.0483491
+---GTAAG-- 0.0444444
+--GGTA---- 0.00896991
+---GT----- 0.000797367
+end consensus
+type 3SS
+center 3
+phase all
+begin consensus
+CAGGTG 143
+CAGGGT 120
+CAGGGC 88
+CAGGGA 82
+CAGGCT 77
+CAGGAG 73
+CAGGGG 66
+CAGGTA 60
+CAGGCC 58
+CAGGAA 54
+CAGATC 50
+CAGCTG 50
+CAGG-C 43.5
+CAGG-T 38.5
+CAGA-C 35.6667
+CAGAT- 29.3333
+CAGA-A 27.3333
+CAG-TC 25.5
+TAGG-G 21.75
+CAG-CA 21.6667
+TAGGA- 21.3333
+TAGGG- 20.6667
+CAGA-G 19.3333
+CAGTG- 18.75
+CAGA-- 18
+TAGG-- 13.8333
+CAG-C- 11.8571
+CAG-T- 10.4
+CAG-A- 7.375
+TAGA-- 6.0625
+TAGC-- 3.3125
+AAGG-- 3.125
+-AGT-- 1.08333
+-AG--- 0.714286
+end consensus
+type 3SS
+center 3
+phase 0
+begin consensus
+CAGGGT 88
+CAGGTG 64
+CAGGAG 43
+CAGGG- 40.3333
+CAGATC 32
+CAGG-C 25
+CAGG-A 19
+CAGG-T 17.3333
+CAGA-C 14.6667
+CAG-TG 13
+CAGAA- 13
+CAGA-T 11.3333
+CAGC-C 10.25
+TAGG-- 9.8125
+CAG--A 4.09091
+CAGT-- 4.45455
+TAG-T- 3.33333
+TAG--- 1.36111
+-AGG-- 1.06061
+-AG--- 0.342857
+end consensus
+type 3SS
+center 3
+phase 1
+begin consensus
+CAGGTG 71
+CAGGCT 36
+CAGGG- 24.75
+CAG-CC 17.5
+CAG-TG 16.6667
+CAGAG- 15.75
+CAGG-- 14.5556
+CAGA-A 13.3333
+CAGTG- 10.75
+CAG-TC 10.3333
+TAGG-G 9.5
+CAGA-- 6.16667
+TAGG-- 5
+CAGC-- 3.69231
+TAG--- 1.66667
+-AG--- 0.328467
+end consensus
+type 3SS
+center 3
+phase 2
+begin consensus
+CAGG-A 19.25
+CAGG-T 14.75
+CAG-G- 4.57143
+CAG--T 4.66667
+TAGG-- 3
+CAG--- 2.87879
+TAG--- 0.645833
+AAG--- 0.25
+end consensus
+type CDS
+phase all
+begin consensus
+AAA 5290.000000
+AAC 4795.000000
+AAG 8178.000000
+AAT 3305.000000
+ACA 6240.000000
+ACC 7728.000000
+ACG 3347.000000
+ACT 4930.000000
+AGA 8491.000000
+AGC 8639.000000
+AGG 8997.000000
+AGT 4417.000000
+ATA 1975.000000
+ATC 4973.000000
+ATG 6474.000000
+ATT 3083.000000
+CAA 7057.000000
+CAC 6815.000000
+CAG 11041.000000
+CAT 5779.000000
+CCA 10537.000000
+CCC 10307.000000
+CCG 5621.000000
+CCT 10134.000000
+CGA 3377.000000
+CGC 5146.000000
+CGG 5375.000000
+CGT 2765.000000
+CTA 3502.000000
+CTC 7465.000000
+CTG 13780.000000
+CTT 5453.000000
+GAA 7461.000000
+GAC 6937.000000
+GAG 9975.000000
+GAT 4949.000000
+GCA 7747.000000
+GCC 10890.000000
+GCG 4828.000000
+GCT 9371.000000
+GGA 10143.000000
+GGC 10400.000000
+GGG 8869.000000
+GGT 5567.000000
+GTA 2143.000000
+GTC 4593.000000
+GTG 8189.000000
+GTT 3021.000000
+TAA 1775.000000
+TAC 3687.000000
+TAG 1333.000000
+TAT 2477.000000
+TCA 6180.000000
+TCC 7668.000000
+TCG 2875.000000
+TCT 5767.000000
+TGA 7315.000000
+TGC 8625.000000
+TGG 11718.000000
+TGT 5197.000000
+TTA 1664.000000
+TTC 5462.000000
+TTG 4420.000000
+TTT 3453.000000
+end consensus
+type CDS
+phase 0
+begin consensus
+AAA 2167.000000
+AAC 2839.000000
+AAG 4830.000000
+AAT 1616.000000
+ACA 1543.000000
+ACC 3187.000000
+ACG 983.000000
+ACT 1484.000000
+AGA 995.000000
+AGC 2722.000000
+AGG 1326.000000
+AGT 1093.000000
+ATA 585.000000
+ATC 3281.000000
+ATG 2538.000000
+ATT 1584.000000
+CAA 1141.000000
+CAC 1981.000000
+CAG 4796.000000
+CAT 1016.000000
+CCA 2021.000000
+CCC 3183.000000
+CCG 1104.000000
+CCT 2289.000000
+CGA 770.000000
+CGC 2011.000000
+CGG 1762.000000
+CGT 687.000000
+CTA 745.000000
+CTC 2964.000000
+CTG 6980.000000
+CTT 1200.000000
+GAA 2729.000000
+GAC 3946.000000
+GAG 6121.000000
+GAT 2318.000000
+GCA 1767.000000
+GCC 4902.000000
+GCG 1288.000000
+GCT 2556.000000
+GGA 2322.000000
+GGC 4338.000000
+GGG 2688.000000
+GGT 1903.000000
+GTA 690.000000
+GTC 2172.000000
+GTG 4546.000000
+GTT 1020.000000
+TAA 0.000000
+TAC 2405.000000
+TAG 0.000000
+TAT 1323.000000
+TCA 990.000000
+TCC 2579.000000
+TCG 684.000000
+TCT 1522.000000
+TGA 0.000000
+TGC 1747.000000
+TGG 1766.000000
+TGT 931.000000
+TTA 397.000000
+TTC 3156.000000
+TTG 1313.000000
+TTT 1697.000000
+end consensus
+type CDS
+phase 1
+begin consensus
+AAA 1534.000000
+AAC 1140.000000
+AAG 2597.000000
+AAT 767.000000
+ACA 3632.000000
+ACC 3429.000000
+ACG 1849.000000
+ACT 2262.000000
+AGA 4427.000000
+AGC 4014.000000
+AGG 5377.000000
+AGT 1927.000000
+ATA 953.000000
+ATC 1055.000000
+ATG 3488.000000
+ATT 777.000000
+CAA 998.000000
+CAC 1332.000000
+CAG 3260.000000
+CAT 731.000000
+CCA 4701.000000
+CCC 3908.000000
+CCG 2252.000000
+CCT 2992.000000
+CGA 471.000000
+CGC 1361.000000
+CGG 1785.000000
+CGT 443.000000
+CTA 825.000000
+CTC 1766.000000
+CTG 4378.000000
+CTT 882.000000
+GAA 924.000000
+GAC 843.000000
+GAG 1897.000000
+GAT 424.000000
+GCA 3140.000000
+GCC 3275.000000
+GCG 1806.000000
+GCT 2595.000000
+GGA 1911.000000
+GGC 2034.000000
+GGG 2835.000000
+GGT 762.000000
+GTA 577.000000
+GTC 968.000000
+GTG 2506.000000
+GTT 563.000000
+TAA 622.000000
+TAC 561.000000
+TAG 912.000000
+TAT 322.000000
+TCA 3963.000000
+TCC 3535.000000
+TCG 1466.000000
+TCT 2607.000000
+TGA 3311.000000
+TGC 4099.000000
+TGG 6194.000000
+TGT 1772.000000
+TTA 773.000000
+TTC 1353.000000
+TTG 2662.000000
+TTT 713.000000
+end consensus
+type CDS
+phase 2
+begin consensus
+AAA 1589.000000
+AAC 816.000000
+AAG 751.000000
+AAT 922.000000
+ACA 1065.000000
+ACC 1112.000000
+ACG 515.000000
+ACT 1184.000000
+AGA 3069.000000
+AGC 1903.000000
+AGG 2294.000000
+AGT 1397.000000
+ATA 437.000000
+ATC 637.000000
+ATG 448.000000
+ATT 722.000000
+CAA 4918.000000
+CAC 3502.000000
+CAG 2985.000000
+CAT 4032.000000
+CCA 3815.000000
+CCC 3216.000000
+CCG 2265.000000
+CCT 4853.000000
+CGA 2136.000000
+CGC 1774.000000
+CGG 1828.000000
+CGT 1635.000000
+CTA 1932.000000
+CTC 2735.000000
+CTG 2422.000000
+CTT 3371.000000
+GAA 3808.000000
+GAC 2148.000000
+GAG 1957.000000
+GAT 2207.000000
+GCA 2840.000000
+GCC 2713.000000
+GCG 1734.000000
+GCT 4220.000000
+GGA 5910.000000
+GGC 4028.000000
+GGG 3346.000000
+GGT 2902.000000
+GTA 876.000000
+GTC 1453.000000
+GTG 1137.000000
+GTT 1438.000000
+TAA 1153.000000
+TAC 721.000000
+TAG 421.000000
+TAT 832.000000
+TCA 1227.000000
+TCC 1554.000000
+TCG 725.000000
+TCT 1638.000000
+TGA 4004.000000
+TGC 2779.000000
+TGG 3758.000000
+TGT 2494.000000
+TTA 494.000000
+TTC 953.000000
+TTG 445.000000
+TTT 1043.000000
+end consensus
+type Intron_Corr_Term
+phase all
+ 65.6094
+type Intron_Corr_Term
+phase 0
+141.429
+type Intron_Corr_Term
+phase 1
+172.738
+type Intron_Corr_Term
+phase 2
+371.127
+type Intron_emission
+begin consensus
+A 399845.000000
+C 371259.000000
+G 393779.000000
+T 425926.000000
+end consensus
+type Pyrimidine_emission
+begin consensus
+A 2299.000000
+C 18610.000000
+G 2345.000000
+T 17132.000000
+end consensus
+type Spacer_emission
+begin consensus
+A 3020.000000
+C 3834.000000
+G 3644.000000
+T 4224.000000
+end consensus
+type Central_Intron_Stay_Prob 
+0.99853
+type Pyrimidine_Stay_Prob 
+0.944485
+type No_Spacer_Prob 
+0.331508
+type Spacer_Stay_Prob 
+0.902704