src/algo/gnomon/gnomon.asn
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--- $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