Python Programming for Biology: Bioinformatics and Beyond

5

Or more generally countable.

6

 Here  !  means  factorial:  the  product  of  a  number  and  all  the  positive  integers  smaller

than it. For example: 6! = 6×5×4×3×2×1.

7

Or strictly speaking observations in the case of a DNA sequence.

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8

 The  use  of  the  term  ‘time’  is  historic,  and  the  chain  needn’t  represent  a  temporal

process.

9

Hence the term model, because we are modelling the state generation mechanism using

transition probabilities.

10

So typically aliphatic or aromatic hydrocarbon.

11

Referred to as underflow.

12

 For  a  better  description  see  Durbin,  R.M.,  Eddy,  S.R.,  Krogh,  A.,  and  Mitchison,  G.

(1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

(1st edn.). Cambridge: Cambridge University Press.

13

See

http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdb.html

.

14

Shrake, A., and Rupley, J.A. (1973). Environment and exposure to solvent of protein

atoms. Lysozyme and insulin. Journal of Molecular Biology 79(2): 351–371.

15

Hubbard, T.J., and Blundell, T.L. (1987). Comparison of solvent-inaccessible cores of

homologous proteins: definitions useful for protein modelling. Protein Engineering  1(3):

159–171.

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