Exercise 2 - Gene Prediction Using Gene Prediction Software
Gene prediction programs combine several steps to predict genes in nucleotide sequences.
Unlike manual gene prediction, which may try to directly tease out a gene from raw sequence by
identifying features like promotors, poly-A signals, splice sites, and open reading
frames, most gene prediction programs try to first narrow down genic areas by examining
the distribution of single nucleotides, as well as di-, tri-, and hexanucleotides.
Apply the gene prediction program
Genscan
to the 1.500-nucleotide sequence. Save your results in a word processor, as entire web pages, and/or as screen shots.
(Should you experience problems with the program, see these input and output shots.)
Try out some other gene prediction programs (e.g. FGENESH, HMM, GRAIL) utilizing the links provided through the
 button above.
Answer the following questions:
- What characteristics does the gene have? (Length, exons, introns, splice sites, promoter, etc.)
- What do the mRNA and amino acid sequences of the gene and its product look like?
Compare your results with those of your manual prediction in Exercise 1.
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