src/algo/gnomon/gnomon.asn

--- $id: $
---
--- Definitions for the Gnomon HMM parameters
---

NCBI-GNOMON DEFINITIONS ::=
BEGIN

Gnomon-params ::= SET OF Gnomon-param

Gnomon-param ::= SEQUENCE {
    gc-content-range SEQUENCE { -- percents
        from INTEGER ,
        to INTEGER } ,
    param CHOICE {
        intergenic Intergenic-params ,
        intron Intron-params ,
        exon Exon-params ,
        start Markov-chain-array ,
        stop Markov-chain-array ,
        donor Markov-chain-array ,
        acceptor Markov-chain-array ,
        coding-region SEQUENCE OF Markov-chain-params , -- three elements (per phase)
        non-coding-region Markov-chain-params } }

Length-distribution-params ::= SEQUENCE {
    step INTEGER ,
    p SEQUENCE OF REAL , -- P(step*(i+.5))|i=0,1,...,N-1
    a REAL , -- Loretz function coefficient for the tail
    l REAL , -- Loretz function coefficient for the tail
    range SEQUENCE {
        min INTEGER ,
        max INTEGER } }

Intergenic-params ::= SEQUENCE {
    initp REAL , -- probability of a genomic point be intergenic
    to-single REAL , -- probability of next gene to be single-exon
    length Length-distribution-params }

Intron-params ::= SEQUENCE {
    initp REAL , -- probability of a genomic point be in an intron
    phase-probabilities SEQUENCE OF REAL , -- 3 elements (per phase)
    to-term REAL, -- probability to be the last 
    length Length-distribution-params }

Exon-params ::= SEQUENCE {
    first-exon-phase-probabilities SEQUENCE OF REAL , -- 3 elements (per end phase)
    internal-exon-phase-probabilities SEQUENCE OF REAL , -- 3*3 elements (begin phase x end phase)
    first-exon-length Length-distribution-params ,
    internal-exon-length Length-distribution-params ,
    last-exon-length Length-distribution-params ,
    single-exon-length Length-distribution-params }

Markov-chain-params ::= SEQUENCE {
    order INTEGER ,
    probabilities SEQUENCE OF -- four elements (per base)
        CHOICE {
        prev-order Markov-chain-params,
        value REAL } }

Markov-chain-array ::= SEQUENCE {
    in-exon INTEGER,
    in-intron INTEGER,
    matrix SEQUENCE OF Markov-chain-params -- in-exon+in-intron elements
    }

END