Python Programming for Biology: Bioinformatics and Beyond

1

Recall that due to splicing variations a single gene can give multiple RNA transcripts.

2

The tight and somewhat stable kind of bond commonly seen between the biologically

abundant elements: carbon, nitrogen, hydrogen and oxygen.

3

Except at absolute zero: −273.15 degrees Celsius or −459.67 degrees Fahrenheit.

4

Fatty soap-like molecules that form double layers.

5

 X-rays  are  chosen  because  their  wavelength  is  on  the  same  scale  as  the  separation

between atoms.

6

Buried or on the surface.

7

 Sali,  A.,  and  Blundell,  T.L.  (1993).  Comparative  protein  modelling  by  satisfaction  of

spatial restraints. Journal of Molecular Biology 234: 779–815.

8

http://www.cambridge.org/pythonforbiology

.

9

The transposed rotation matrix is the last argument so it operates on the (X, Y, Z) spatial

dimension of the data, rather than the (long) atom dimension.

10

The y axis has the first and last numbers, x and z, set to 0 and the middle number, for y,

varies.

11

As a Python list of lists this would be [[1,0,0],[0,1,0],[0,0,1]].

12

This is simply applying Pythagoras’ rule for calculating the length of the hypotenuse of

a right-angle triangle in three dimensions.