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Exercise 12.1
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Basic string matching. Write a program that
looks for a query string in a target string. For instance, if the
query string is "gone", it finds a match at position 22
of the target string "goof through the way-gone-osphere."
Don't use regular expressions or any of Perl's built-in
string-matching abilities; instead, examine individual positions in
the strings, compare characters, and invent your own algorithm.
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Exercise 12.2
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Explore the NCBI BLAST web pages at http://www.ncbi.nlm.nih.gov/BLAST. Familiarize
yourself with the purpose and use of the various component programs
and read the tutorial information on the meaning of the statistics.
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Exercise 12.3
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Explore the Bioperl web pages at http://www.bioperl.org. Download the code and
install it on your computer.
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Exercise 12.4
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Perform BLAST searches at the NCBI web site. Search with DNA against
DNA databases; then search with the same DNA against protein
databases, and compare the output.
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Exercise 12.5
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Perform two BLAST searches with related sequences. Parse the BLAST
output of the searches and extract the top 10 hits in the header
annotation of each search. Write a program that reports on the
differences and similarities between the two searches.
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Exercise 12.6
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Write a program that uses Bioperl to perform a BLAST search at the
NCBI web site, then use Bioperl to parse the BLAST output.
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Exercise 12.7
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Using Bioperl modules mixed with your own code, write a program that
runs BLAST on a set of DNA sequences and saves the IDs of the list of
hits of each BLAST run sorted in arrays. Allow the user to view each
list, to view hits in common between multiple lists and hits unique
to one of multiple lists. For each hit, enable the user to fetch its
entire GenBank record.
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Example 12.8
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Write an explanation of the code for the subroutine
extract_HSP_information. Be sure to refer to the
format of the data the code uses as input.
