Gene Prediction

1. Download Hm_dna.fa from
   http://www.tbi.univie.ac.at/~xtof/Leere/300632/Data/2802_Hm_dna.fasta

2. Go to GeneMark (frame-by-frame) http://exon.gatech.edu/genemark/fbf.cgi and upload Hm_dna.fa. Choose B. subtilis as closest species (Running Options)
3. save the results on you computer
4. Convert the fasta file (.fa) to GenBank format (.gb) with the tool Readseq
   http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi. Now the sequence has line numbering.
5. Can you find the Shine-Dalgano sequence (AGGAGG) in each frame predicted by GeneMark?
6. Do another gene prediction predict with Glimmer, a IMM (interpolated markhov model) based model Glimmer v3.

7. Upload Hm_dna.fa, select ``Glimmer Genes'', choose ``B. subtilis'' as closest species
8. Retrieve results by clicking "Get Summary'', the select ``Text Table''.
9. Compare the results from both prediction, especially the boundaries of the predicted genes (start-end) and their orientation. Which program predicts more genes and how would you explain this?