Bioinformatics - Finding ORF Genes: Annotating a viral genome
Purpose: to identify the genes in a viral genome by finding ORFs, to determine the nature of the
potential genes, and to identify the nature of the virus
ORF-finding
1. Open Gene Boy at http://www.dnai.org/geneboy/index.html
2. On the left, under 'Sequences', select 'Genome'
3. How long is the sequence?
o On the right, under 'Operations', select 'Find Genes', then 'ORF'
o Below the window select 'Reverse'
o Explain what you see on the screen answering these questions:
o What do the three horizontal bars represent?
o What do the yellow and green boxes represent?
o What constitutes an ORF?
o Why are you searching for ORFs?
o What does 'Reverse' do?
o Why is this function needed?
o Complete the table below
Frame
From
To
Length
Organism
Gene
Gene verification and identification
1. Go to the DNAi website at http://www.dnai.org/index.htm
2. Select 'Genome', then 'Genome Mining', then 'Gene Finding'
3. Click the forward icon until you arrive at frame #4
4. Compare your ORF results with the genome map of this virus for reading frame 1 (RF1);
did you find all ORFs that the map shows?
5. What are the genes?
6. Click the forward button and examine reading frame 2 (RF2) Did you detect the gene in
the map through ORF Find? Why not? Which gene is it?
7. Select the forward button, and examine reading frame 3 (RF3). How many ORFs did you
find in RF3? How many genes does the map show? Why the discrepancy? What are the
genes in RF3?
8. What organism is the genome derived from?
9. Find a complete map of this virus' genome at
http://www.dnalc.org/bioinformatics/Resources/hiv_hxb2_map.pdf What new details
does this map provide?
10. Find the two splice HIV genes in the map. Which one's are they?
11. How could you find out what functions the different genes have?