[Biojava-l] Dp newbie question!!

[alex johansson]

Hi,

Iam a Cell biology student with a growing interest in biojava, although i
have a very basic biojava experience but the cookbook
examples makes it easy to get around with api. My question is very basic and
might sound very stupid, i followed the cookbook example on creating a HMMER
like profileHMM and made a profile with a set 12 training sequences (19bp)
and tested it with a test sequence with motif occuring twice.Below is the
output from the program:

Log Odds = 43.786769243019506
m-1 m-2 m-3 m-4 m-5 m-6 d-7 m-8 m-9 m-10 m-11 m-12 m-13 m-14 m-15 m-16 m-17
d-18 i-18 d-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19
i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 i-19 m-20 i-20

My Question is how to interpret these results?how do i know if the motif is
occuring twice and its location in the test sequence?? I know that 'm'
stands for match and 'i' and 'd' stands for insert and delete transitions in
the path from start to end.

I'd certainly appreciate if the biojava gurus out there could spend some of
their valuable time in explaining this.

Thank you for your time,

Cheers,
Alex J