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Introduction to wEMBOSS

Friday May 11, 2007

Use the EMBOSS/wEMBOSS tools and environment to answer the following question.

Please note all intermediary steps you used to reach the final results (with details for all non-default parameters).

 

 

Exam
You receive 3 protein sequences and the 3 mRNA associated sequences.

You would like to derive primers found in regions common to all 3 mRNA sequences aligned using the protein sequences as guides.

a) do a multiple sequence alignment (MSA) of the 3 proteins (emma)

b) align the DNA sequences over the protein MSA (tranalign).

c) derive a consensus for perfectly conserved regions (cons).

d) extract 5 potential primer pairs (eprimer3)

Give the 5 pairs and the positions of the amplified fragment (print eprimer3 results).

What is the size of the largest amplified fragment?

 

 

Latest update 2007-05-11
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