Python Programming for Biology: Bioinformatics and Beyond

A basic introduction to sequence variation

Naturally the genetic codes of different kinds of organism differ to support their different

construction,  habits  and  biological  requirements.  Also,  genetic  codes  vary  between

individuals of the same species, despite the large degree of similarity that binds them as a

species.  It  is  such  variation  within  species  that  provides  the  opportunity  for  offspring  to

differ from their parents and potentially gain an improvement or specialisation, which in

time may give rise to a new species. In a more modern context, sequence variations have a

vital  role  in  our  understanding  of  genetic  diseases  and  are  becoming  increasingly

important for the development of pharmaceuticals, where the effectiveness and side effects

of drugs may vary significantly according to the genotype of a person.

The variety of species and individuals is all down to the variety of genome sequences,

but in order to discover as much as we can about the consequences of and reasons for this

variation we should understand something about the mechanism by which sequences can

change.  In  this  chapter  we  will  not  go  in  to  immense  detail  about  the  underlying

mechanics, but simply cover the main principles and, importantly as far as bioinformatics

is concerned, describe what kinds of change are detectable in the biological sequences. It

should  be  remembered  that  it  is  only  changes  that  are  passed  on  to  offspring  which  will

influence  evolution  directly,  but  other  variations  may  be  important,  for  example,  in  the

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study of cancer-causing mutations.