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Computational Genomics

Code and examples for JHU Computational Genomics class. Please feel free to submit issues.

Concept notebooks

The notebooks subdirectory contains the raw JSON for the iPython notebooks referenced in class. The notebooks are also available as public GitHub gists and you can view readable versions of them at the following URLs:

These are for teaching purposes. They are certainly not meant to be efficient. Please feel free to submit issues.

File format notebooks

The following notebooks describe and explore some common file formats used to store genomics data. They also include Python code for parsing (and sometimes indexing) the formats.

Other class resources

If you are taking my class and you have any trouble accessing these resources, please contact me and I can help. All of these articles should be easily accessible from the JHU campus or via VPN / library proxy.

Possible notebook additions

  • Boyer-Moore
  • Higher-order HMM
  • Spliced alignment
  • Minimum path cover on DAG to recover isoforms
  • Pair HMMs
  • Profile HMMs