Python Programming for Biology: Bioinformatics and Beyond

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PEP8:

https://www.python.org/dev/peps/pep-0008/

.

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From Python 2.5.

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With a 3.2-GHz 64-bit AMD processor.

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If we use the original math import we could do sqrt = math.sqrt.

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A callable object.

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Some might say infinite.

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 A  new-style  class  in  Python  2  would  be  defined  using  class  Something(object):.  In

Python 3 all classes are new style and do not need to subclass object.

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Biological sequences

Contents

Bio-molecules for non-biologists

Proteins

DNA

Transcription

Translation

DNA sequencing

Using biological sequences in computing

Translate a DNA sequence into protein

Estimate molecule mass

Simple sub-sequence properties

Finding a sequence motif

GC content of DNA

Protein hydrophobicity plot

Measuring repetitiveness

Protein isoelectric point

Obtaining sequences with BioPython

Reading and writing FASTA files

Accessing public databases