programming-for-dummies

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Searching Databases
Mutation and concatenation are just two ways to manipulate molecular structures
within a computer. If you created half a DNA sequence, you still need to
determine the other half. Because DNA consists of two strands bound together
in a double helix form, it’s easy to determine the second sequence of DNA after
you know the first one. That’s because each adenine (A) links up with thymine
(T) and each cytosine (C) links up with guanine (G).
The two strands of DNA are complimentary sequences. To calculate a complimentary
sequence by knowing only one of the sequences, you can use a
simple program that replaces every A with a T, every C with a G, every T with
an A, and every G with a C. A Perl program to do this might look like this:
$DNA = ‘ACTGTTG’;
$compDNA = tr/ACGT/TGCA/;
The tr command simply tells Perl to translate or swap one character for
another. So the above tr/ACGT/TGCA/; command tells Perl to translate every
A into a T, every C into a G, every G into a C, and every A into a T all at once.
The second step in determining a complimentary sequence is to reverse the
order of that sequence. That’s because sequences are always written a specific
way, starting with the end of the sequence known as 5’ phosphoryl (also
known as 5 prime or 5’) and ending with 3’ hydroxyl (known as 3 prime or
3’). So to display the complimentary sequence correctly, you have to reverse
it using this Perl command:
$DNA = ‘ACTGTTG’;
$compDNA = tr/ACGT/TGCA/;
$revDNA = reverse $compDNA;
It’s important to know both sequences that make up a DNA strand so you
can use both DNA sequences to search for information. When faced with an
unknown structure, there’s a good chance someone else has already discovered
this identical molecular structure. So all you have to do is match your molecular
structure with a database of known structures to determine what you have.
Searching Databases
After biologists discover a specific molecular structure, they store information
about that sequence in a database. That way other biologists can study that
sequence so everyone benefits from this slowly growing body of knowledge.
Unfortunately, there isn’t just one database, but several databases that
specialize in storing different types of information:
✦ GenBank stores nucleotide sequences.