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Exercise 9.1
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Modify Example 9-3 to accept DNA from the command
line; if it's not specified there, prompt the user for a FASTA
filename and read in the DNA sequence data.
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Exercise 9.2
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Modify Exercise 9.1 to read in, and make a hash of, the entire REBASE
restriction site data from the bionet file.
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Exercise 9.3
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Modify Exercise 9.2 to store the REBASE hash created in a DBM file if
it doesn't exist or to use the DBM file if it does exist. (Look
ahead to Chapter 10 for more information about
DBM.)
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Exercise 9.4
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Modify Example 5-3 to report on the locations of the
motifs that it finds, even if motif appears multiple times in the
sequence data.
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Exercise 9.5
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Include a graphic display of the cut sites in the restriction map by
printing the sequence and labeling the recognition sites with the
enzyme name. Can you make a map that handles multiple restriction
enzymes? How can you handle overlapping restriction sites?
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Exercise 9.6
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Write a subroutine that returns a restriction digest, the fragments
of DNA left after performing a restriction reaction. Remember to take
into account the location of the cut site. (This requires you to
parse the REBASE bionet in a different manner.
You may, if you wish, ignore restriction enzymes that are not given
with a ^ indicating a cut site.)
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Exercise 9.7
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Extend the restriction map software to take into account the opposite
strand for nonpalindromic recognition sites.
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Exercise 9.8
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Given an arithmetic expression without parentheses, write a
subroutine that adds the appropriate parentheses to conform to
Perl's precedence rules. (Warning: this is a pretty hard
exercise and should be skipped by all but the true believers who have
extra time on their hands. See the Perl documentation for the
precedence rules.)
