Solution For The Exercises on The Alignment of Two Sequences

1.

2-Tryptophan and Methionine are only represented by one codon both. This means that any one point mutation will turn them into something else. In contrast, Valine is insensitive to a mutation on the third position.

3-The main diagonal on a substitution matrix is an indicator of the rate of mutation observed for an amino-acid. A high value indicates that a residue is likely to remain unchanged throught evolution. Tryptophan (W) is traditionnally the most conserved residue. This is a constrast with the genetic code.
This means that the selection of mutation follows rules that are not only statistical. For instance, the substitution of a tryptohan by some other residue is often very destabilizing for a protein structure. As a consequence, even if that type of mutation is frequent, occurences were the mutation gets selected are very rare.

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4.

       1.The big square spot is a low-complexity region, as it happens a serine-rich
          region.
       2.It is a mature mRNA plotted against the corresponding gene. The
          interruptions in the diagonal are introns.
       3.It's a lab artifact: during the reverse transcription of an mRNA (an EST, in
          that case), the reverse transcriptase did a U-turn, so that the end of the
          cDNA is the reverse complement of its start (this is why you see a second
          diagonal). This is an example of why you should be careful with EST data.
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5.

1-This sequence contains nine repeats, all homologous to one another, hence the stripes observed on the plot.

2-Lalign produces by default the 10 best non-overlapping alignments. None of them gives you the coordinates of the repeats, but by extrapolation it is possible to find a near exact solution of:

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