.
For I = TTGGAATACCATC and J = GGCATAATGCACCCC, make dot
matrices for the k-tuple hits for k = 1, 2, and 3.
.
The E. coli F plasmid transfer origin region contains the sequence
I:
5_-ATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTT
AAAAAAGCG-3_
The TraY protein has been shown to bind to a region some 1600 bp away at
a site that contains the sequence
J:
5_-TAACACCTCCCGCTGTTTAT-3_
Perform dot-matrix analyses for k = 1 and k = 2 to locate in I a subsequence
that is similar to J. This identifies a potential binding site for TraY in sequence
I. [Hint: Use R to construct a matrix having dimensions determined
by the lengths of J and I, initialize elements to zero, and then substitute the
appropriate elements with the number 1 to indicate matches. Produce two
matrices: one for k = 1 and another for k = 2.]