1--- $id: $ 2--- 3--- Definitions for the Gnomon HMM parameters 4--- 5 6NCBI-GNOMON DEFINITIONS ::= 7BEGIN 8 9Gnomon-params ::= SET OF Gnomon-param 10 11Gnomon-param ::= SEQUENCE { 12 gc-content-range SEQUENCE { -- percents 13 from INTEGER , 14 to INTEGER } , 15 param CHOICE { 16 intergenic Intergenic-params , 17 intron Intron-params , 18 exon Exon-params , 19 start Markov-chain-array , 20 stop Markov-chain-array , 21 donor Markov-chain-array , 22 acceptor Markov-chain-array , 23 coding-region SEQUENCE OF Markov-chain-params , -- three elements (per phase) 24 non-coding-region Markov-chain-params } } 25 26Length-distribution-params ::= SEQUENCE { 27 step INTEGER , 28 p SEQUENCE OF REAL , -- P(step*(i+.5))|i=0,1,...,N-1 29 a REAL , -- Loretz function coefficient for the tail 30 l REAL , -- Loretz function coefficient for the tail 31 range SEQUENCE { 32 min INTEGER , 33 max INTEGER } } 34 35Intergenic-params ::= SEQUENCE { 36 initp REAL , -- probability of a genomic point be intergenic 37 to-single REAL , -- probability of next gene to be single-exon 38 length Length-distribution-params } 39 40Intron-params ::= SEQUENCE { 41 initp REAL , -- probability of a genomic point be in an intron 42 phase-probabilities SEQUENCE OF REAL , -- 3 elements (per phase) 43 to-term REAL, -- probability to be the last 44 length Length-distribution-params } 45 46Exon-params ::= SEQUENCE { 47 first-exon-phase-probabilities SEQUENCE OF REAL , -- 3 elements (per end phase) 48 internal-exon-phase-probabilities SEQUENCE OF REAL , -- 3*3 elements (begin phase x end phase) 49 first-exon-length Length-distribution-params , 50 internal-exon-length Length-distribution-params , 51 last-exon-length Length-distribution-params , 52 single-exon-length Length-distribution-params } 53 54Markov-chain-params ::= SEQUENCE { 55 order INTEGER , 56 probabilities SEQUENCE OF -- four elements (per base) 57 CHOICE { 58 prev-order Markov-chain-params, 59 value REAL } } 60 61Markov-chain-array ::= SEQUENCE { 62 in-exon INTEGER, 63 in-intron INTEGER, 64 matrix SEQUENCE OF Markov-chain-params -- in-exon+in-intron elements 65 } 66 67END