Python Programming for Biology: Bioinformatics and Beyond

7

See

Chapter 15

for discussion.

8

Although strictly speaking not all DNA substitutions are equally likely.

9

A bad, but probably intentional, pun; ‘N-y’ for ‘any’. Such ambiguities are often caused

by uncertainties in the recording of sequences, especially at the ends of a DNA read.

10

 Sixty-two  is  the  percentage  sequence  identity  limit  of  the  blocks  of  multiply  aligned

sequences that are used to count the substitutions.

11

This isn’t universally true for all substitution matrices though.

12

Dayhoff, M.O., Schwartz, R., and Orcutt, B.C. (1978). A model of evolutionary change

in  proteins.  Atlas  of  Protein  Sequence  and  Structure  (volume  5,  supplement  3  ed.).

Washington DC: National Biomedical Research Foundation. pp. 345–352.

13

Henikoff, S., and Henikoff, J.G. (1992). Amino acid substitution matrices from protein

blocks. PNAS 89(22): 10915–10919.

14

Needleman, S.B., and Wunsch, C.D. (1970). A general method applicable to the search

for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology

48(3): 443–453.

15

 Smith,  T.F.,  and  Waterman,  M.S.  (1981).  Identification  of  common  molecular

subsequences. Journal of Molecular Biology 147: 195–197.

16

 See  the  description  of  list  comprehensions  in

Chapter  4

 for  an  explanation  of  the

Python.

17

 Altschul,  S.,  Gish,  W.,  Miller,  W.,  Myers,  E.,  and  Lipman,  D.  (1990).  Basic  local

alignment search tool. Journal of Molecular Biology 215(3): 403–410.

18

The equivalent in the older BLAST2 package is ‘formatdb’

19

Regular expressions are discussed more fully in

Appendix 5

.

20

 eXtensible  Markup  Language:  a  text-based  general  data  storage  format,  somewhat

similar to the HTML used in web pages.

21

For full details of all the options available see the BLAST+ package documentation in

the help section at the NCBI:

http://blast.ncbi.nlm.nih.gov

.

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