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Now we can use transeq to translate that region and use the translated peptide for some further analyses.

There are several ways to verify your translation is correct. You could retrieve the conceptual translation from the GenBank entry at NCBI and use needle to align the sequences, or use tblastn to see if your translated sequence is found in the translated database.

Exercise 7 - transseq

Use transseq to translate the human globin mRNA sequence. Since we only want to translate the ORF that works, select that ORF.

Does the protein you see translated appear to have more than one stop (*)? What is the region between the start and stop codon that you defined earlier: Change the parameter “Regions to translate” to the region you identified using the getorf program. Experiment with that parameter. What do you observe?

Save this translated sequence from the first (M) to the last (H) residue. You will be using it in subsequent pages of this workshop.

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Page last modified September 29, 2008