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