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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
