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    Biology: DNA Code and Sequence Alignments

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    1. You clone a double stranded DNA fragment from a pathogenic fungal stain. You suspect that the fragment contains a gene encoding a Seven Amino Acid Peptide.

    Here's one of the DNA strand fragments:

    5' T G A G A T G C T T A G C T G C A A A C C T A T T T A A A C 3'

    A) What's the amino acid sequence of this peptide?
    B) What's the (CAI) of the gene encoding peptide?
    C) Does the calculated (CAI) value support the hypothesis that the gene encoding the seven amino acid peptide is likely to be foreign gene? Explain.

    2. Here are (4) protein sequences w/ multiple sequence alignments:


    P1: REACWS
    P2: REECWA
    P3: -DACWS
    P4: KDNCFT

    K = 123456

    A) Use the Sum-of-Pairs method to calculate the score of the first column (k=1) of the alignment, using BLOSUM62 and the following gap scores:

    s [x , -] = s [- , y] = -2 ; s [- , -] = 0

    B) Use the Average Score Method to answer the following questions:

    Calculate the profile value for the amino acid D at position k = 2 in the alignment.

    M2D =

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    Solution Preview

    A) Met L S C K P I Stop
    B) CAI value is 0. 356
    C) Low expressed or foreign genes (CAI < 0.15). So it is not likely to be a foreign gene.

    Using the BLOSUM 62 scoring matrix and the above gap penalties,
    Sum of pairs for the first column would be calculated as :

    SP(m1) = S (R,R) + S(R,-) ...

    Solution Summary

    The solution examines DNA codes and sequence alignments. It describes the amino acid sequence of the peptide provided.