Running example: DNA and amino acid motifs

Bioinformatics uses computational methods to ask biology questions; a great deal of bioinformatics has to do with DNA, RNA, and genomic sequencing. It’s a common activity to look for particular sequences in a list of DNA or RNA bases, or to look for particular “motifs” in sequences of bases or the amino acids they encode.

As our running example, we’ll be thinking about DNA and amino acid motifs. By way of reminder, the DNA bases are:

• cytosine, written C

• guanine, written G

• adenine, written A

• thymine, written T

Every three DNA bases is a codon denoting a particular amino acid (or the STOP code); Wikipedia has a nice table explaining the encoding.

To work with DNA and amino acids in Python, we can encode them as strings. For DNA, it’s straightforward: “CGA” corresponds to the DNA strand containing cytosine, guanine, and then adenine.

For amino acids, it’s slightly more complex. We can use the IUPAC notation for the amino acids we’ll see:

A     Alanine
C     Cysteine
D     Aspartic acid
E     Glutamic acid
F     Phenylalanine
G     Glycine
H     Histidine
I     Isoleucine
K     Lysine
L     Leucine
M     Methionine
N     Asparagine
P     Proline
Q     Glutamine
R     Arginine
S     Serine
T     Threonine
V     Valine
W     Tryptophan
Y     Tyrosine
_     Translation stop

So 'NRSA' represents the sequence of amino acids Asparagine, Arginine, Serine, Alanine.