sample.hmm

#state character definition//accepted inputs and the accompanying emission probabilities
                           //test multiline comment
A|1->A
T|1->T
C|1->C
G|1->G //comment here too
N|.25->A;.25->T;.25->C;.25->G
#end scd

#model structures
>1|Pre-gene//expect 25 nt before the gene starts
1|N|.96->1;.04->2
#

>2|Promoter//find some form of a TATA box
           //another random comment test
1|T|1->2
2|A|.2->3;.8->4
3|A|1->4
4|T|1->5
5|A|.1->6;.8->7;.1->8 //another comment
6|A|.5->7;.5->8
7|T|1->8
#

>3|Interim region//4 nt gap
1|N|1->2
2|N|1->3
3|N|1->4
4|N|1->5
#

>4|Ribosomal region//find a spot for the ribosome to stick to
1|A|1->2
2|A|.7->3;.3->5
3|T|.4->4;.6->5
4|T|1->5
5|T|1->6
6|G|1->7
#

>5|Start Codon//(ATG==Methionine)
1|A|1->2
2|T|1->3
3|G|1->4
#

>6|Coding region//expect about 100 codons in the gene
1|N|1->2
2|N|1->3
3|N|.99->1;.01->4
#

>7|Stop codon//(TAG==amber,TAA==ochre,TGA==opal or umber)
1|T|.7->2;.3->3
2|A|.5->4;.5->5
3|G|1->4
4|A|1->6
5|G|1->6
#

>8|Termination region//sequence to unstick the ribosome
1|T|1->2
2|T|1->3
3|T|1->4
4|N|1->5
5|N|1->6
6|N|1->7
7|A|1->8
8|A|1->9
9|A|1->10
#

>9|Post-gene//any number of nts after the gene is ok
1|N|1->1#
#end model