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5.8. Exercises

Exercise 5.1

Use a loop to write a nonhalting program. The conditional must always evaluate to true, every time through the loop. Note that some systems will catch that you're in an infinite loop and will stop the program automatically. You will stop your program differently, depending on which operating system you use. Ctrl-C works on Unix and Linux, a Windows MS-DOS command window, or a Mac OS X shell window.

Exercise 5.2

Prompt the user to enter two (short) strings of DNA. Concatenate the two strings of DNA by appending the second to the first using the .= assignment operator. Print the two strings as concatenated, and then print the second string lined up over its copy at the end of the concatenated strings. For example, if the input strings are AAAA and TTTT, print:


Exercise 5.3

Write a program that prints all the numbers from 1 to 100. Your program should have much fewer than 100 lines of code!

Exercise 5.4

Write a program to calculate the reverse complement of a strand of DNA. Do not use the s/// or the tr functions. Use the substr function, and examine each base one at a time in the original while you build up the reverse complement. (Hint: you might find it easier to examine the original right to left, rather than left to right, although either is possible.)

Exercise 5.5

Write a program to report on the percentage of hydrophobic amino acids in a protein sequence. (To find which amino acids are hydrophobic, consult any introductory text on proteins, molecular biology, or cell biology. You will find information sources in Appendix A.)

Exercise 5.6

Write a program that checks if two strings given as arguments are reverse complements of each other. Use the Perl built-in functions split, pop, shift, and eq (eq is actually an operator).

Exercise 5.7

Write a program to report how GC-rich some sequence is. (In other words, just give the percentage of G and C in the DNA.)

Exercise 5.8

Modify Example 5-3 to not only find motifs by regular expressions but to print out the motif that was found. For example, if you search, using regular expressions, for the motif EE.*EE, your program should print EETVKNDEE. You can use the special variable $&. After a successful pattern match, this special variable is set to hold the pattern that was matched.

Exercise 5.9

Write a program that switches two bases in a DNA string at specified positions. (Hint: you can use the Perl functions substr or splice.

Exercise 5.10

Write a program that writes a temporary file and then deletes it. The unlink function removes a file: just say, for example:

unlink "tmpfile";

but also check to see if unlink is successful.


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