Download Bioinformatics programming exercise II

Bioinformatics programming exercise II
1.
a. Write a program that asks the user to input a DNA sequence!
Enter the sequence: ‘ggAcgCgaggcCAca’ and assign it to the variable
dna.
As sequences (dna, rna, protein) can occur in lowercase characters or
else in uppercase characters (or even mixed), one may wish to format
the output of a program.
b. Change the case of all characters to lowercase and display the whole
sequence on the screen! Now do the same thing with uppercase!
Replication:
The special structure of the DNA (deoxyribonucleic acid) allows stored
information to be preserved and passed from one cell to another (cell
division). The strands of DNA’s famous double helix structure are held
together by nucleotide bonds, where A (Adenine) only binds with T
(Thymine) and G (Guanine) always with C (Cytosine). Scientists say that
each strand of the double helix is a chemical “mirror image” of its vis-àvis. When cells divide, the two strands of the double helix will be
separated and each of them works as a template for building the
complementary strand in the daughter cell.
2.
a. Imagine our DNA sequence from a) and b) is a single strand and waits
for bases to bind and build the chemical mirror strand. Write a
subroutine that builds and returns the complement of a nucleotide
sequence!
(hint: check the Perl – Quick Reference to learn, how to build a
subroutine in Perl)
b. Pass our sequence as argument to the new function and print out the
newly created double helix like this:
dna sequence: aagctatgtctg
||||||||||||
complement:
xxxxxxxxxxxx
(hint: use \t for tabulator and \n for newline, to format your output)
Transcription:
DNA can also act as template for the production of the molecule RNA
(ribonucleic acid). The code is produced from one strand of the DNA by
a process called "transcription". The product of a transcription is called
messenger RNA and it consists of the nucleotides A, G, C and U
(Uracil; which replaces Thymine). mRNA is sent out of the nucleus
where the message is translated into proteins.
3.
a. Write a function that transcribes DNA into RNA (A binds with U and G
with C)!
b. Pass our sequence as argument to the new function and print out the
result like this:
DNA: aagctatgtctg
||||||||||||
RNA: xxxxxxxxxxxx
Translation:
Translation of mRNA into protein is the final step in gene expression.
Where DNA is a polymer build from nucleotides (4 types) the protein is
made of amino acids (20 types). The genetic code provided by the DNA
will be translated to the protein, therefore 3 bases (a codon) build the
code for one amino acid. There are totally 64 possible ways to combine
3 nucleotides (43=64) to a codon.
Some codons are redundant, others have a special function of telling
the cell’s translation machinery to stop a mRNA molecule (see the
codon table).
4.
a. Copy the codon table and the translation routine from your first exercise
and put the routine into a function environment!
b. Pass the DNA sequence as argument to the new function and print out
the result like this:
DNA: aagctatgtctg
||||||||||||
RNA: xxxxxxxxxxxx
\|/\|/\|/\|/
AAS: x x x x