Python Programming for Biology: Bioinformatics and Beyond

7

http://gmod.org/wiki/GFF3

.

8

National Center for Biotechnology Information in the United States.

9

Binary mode is used because response.read in Python 3 always gives data bytes and in

any case we could be dealing with a compressed file (e.g. GZIP).

10

Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-

efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):

R25.

11

Li,  H.,  and  Durbin,  R.  (2009).  Fast  and  accurate  short  read  alignment  with  Burrows-

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Wheeler Transform. Bioinformatics 25: 1754–1760.

12

http://www.ncbi.nlm.nih.gov/geo/

.

13

Download via:

http://bowtie-bio.sourceforge.net

.

14

 Li,  H.,  Handsaker,  B.,  Wysoker,  A.,  et  al.;  1000  Genome  Project  Data  Processing

Subgroup  (2009).  The  Sequence  Alignment/Map  format  and  SAMtools.  Bioinformatics

25(16): 2078–2079.

15

http://www.cambridge.org/pythonforbiology

.

16

http://pypi.python.org/pypi/HTSeq

.  Note  that  to  install  this  you  can  use  the  Python

setup  tool  by  issuing  the  following  at  the  command  line:  python  setup.py  build;  python

setup.py install.

17

A Python wrapper for SAMtools:

http://pypi.python.org/pypi/pysam

.

18

 We  could  also  find  data  that  relates  to  the  Ensembl  database  at  an  alternative  site:

ftp://ftp.ensembl.org/pub/current_gtf/

;  note  GTF  and  GFF  formats  are  generally

compatible, the former being a more restricted set of the latter.

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