Math 297/Biol 497

Biomolecular Computing in Nature

Assignment 6

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The micronuclear versions of a number of Oxytricha trifallax (=Sterkiella histriomuscorum) genes are available under the accession numbers (following links):

Gene

Link
MIC - Actin I

U19288
MIC - DNA polymerase alpha

DQ525914, U89697

MIC - alpha Telomere binding protein

AF067830
MIC - beta tubulin

AY116145
MIC - beta Telomere binding protein

 EU047941, EU047939

For each of these genes:

  1. For each of these genes carefully tabulate the pointer sections of MDSs and the pointers' bp lengths. Is there a correlation between the pointer lengths and the level of scrambling of the MDSs in the corresponding IC genes?

  2. For each of these genes tabulate the IESs and their bp lengths. Is there a corellation between IES lengths and MDS lengths?

  3. Determine the total number of nucleotides in a single strand of these MIC genes.

  4. Determine the number of "A", "C", "T" and "G" nucleotides in a single strand of each of these MIC genes.

  5. Determine the number of each nucleotide pairs "MN" where M, N are A, C, T or G, in a single strand of these MIC genes.

  6. Determine for each IES the number of "A", "C", "T" and "G" nucleotides in a single strand.

  7. Determine for each IES the number of each nucleotide pairs "MN" where M, N are A, C, T or G, in a single strand.