Python Programming for Biology: Bioinformatics and Beyond

1

Remember in Python 2 dividing two whole numbers gives a whole number.

2

 Altschul,  S.F.,  Madden,  T.L.,  Schäffer,  A.A.,  Zhang,  J.,  Zhang,  Z.,  Miller,  W.,  and

Lipman,  D.J.  (1997).  Gapped  BLAST  and  PSI-BLAST:  a  new  generation  of  protein

database search programs. Nucleic Acids Research 25: 3389–3402.

3

We could alternatively have used insert(0) to add to the start of the lists, though the way

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we have shown is quicker.

4

Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTAL W: improving the

sensitivity  of  progressive  multiple  sequence  alignment  through  sequence  weighting,

position specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22):

4673–4680. Download via

http://www.clustal.org/

.

5

 Edgar,  R.C.  (2004).  MUSCLE:  multiple  sequence  alignment  with  high  accuracy  and

high throughput. Nucleic Acids Research 32(5): 1792–1797.

6

Notredame, C., Higgins, D.G., and Heringa, J. (2000). T-Coffee: a novel method for fast

and  accurate  multiple  sequence  alignment.  Journal  of  Molecular  Biology  302(1):  205–

217.