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This section will introduce you to a few of the EMBOSS applications that can be used to analyze protein sequences. Obviously, the pairwise sequence comparison methods illustrated in the previous pages with nucleic acid sequences can also be used with protein sequences.

Some simple EMBOSS applications translate your cDNA sequence into protein; others predict possible open reading frames from genomic DNA sequences.

If we start with genomic DNA sequences, first we need to identify our open reading frame. Since a DNA sequence may be transcribed from either strand and translation could begin in any of three positions, there are six possible reading grames. We can get a rapid visual overview of the distribution of ORFs in the six frames of our sequence using the EMBOSS program plotorf. getorf is another program in EMBOSS that will identify the potential start and end points of open-reading frames.

Exercise 6 - plotorf and getorf

A) Use plotorf (under Nucleic Gene Finding) to plot the mRNA from human globin. Remember, this is an mRNA molecule. W hich open-reading frame do you think is the correct one?

B) Use getorf to plot the same sequence. Change the parameter "Type of output" to display the DNA sequence between the start and stop codons. What is the actual start and stop position of the ORF you identified in plotorf?

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Page last modified September 29, 2008