Class Session 13

Topics covered

• Using Python to build a bioinformatics pipeline

Slides

• None

Hands-on Documents

• class13-python-pipelines.pdf

Data sets for hands on and homework

• unknown1.fas
• unknown2.fas
• unknown3.fas

Assignments

• See the hand-out for in-class assignments 13.1 and 13.2, DUE AT THE END OF CLASS
  • email your IPython notebooks to Paul

Readings

• HMMER -- "HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments."
  • Profile Hidden Markov Models. S. R. Eddy. Bioinformatics, 14:755-763, 1998.
  • The above paper is the original reference. See the HMMER web page for more recent refs.
• MAFFT
  • Katoh, Misawa, Kuma, Miyata 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
  • The above paper is the original reference. See the MAFFT web page for more recent refs.

Soundtrack