Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/ucsb_hamster/lib/wisecfg/human.gp @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/orthologs/ucsb_hamster/lib/wisecfg/human.gp Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,543 @@ +# 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 + +