This repository describes computational work associated with a study led by Hui-Ling Yen to examine influenza transmission in ferrets. The computational work is performed by Jesse Bloom.
The work is performed in a set of iPython notebook\s. The Notebooks listed below describe each analysis. The Input data files_ are also detailed below.
Each of the following is an iPython notebook_ describing a particular analysis:
SequenceAnalysisAndSynonymousBarcoding.ipynb <SequenceAnalysisAndSynonymousBarcoding.ipynb> describes an analysis of the A/California/04/2009 pdmH1N1 sequences in Hui-Ling Yen\'s reverse-genetics plasmids, and the design of synonymously barcoded variants.The ./sequences/ subdirectory contains sequences.
all_pdmH1N1_seqs.fasta contains all full-length human H1N1 sequences annotated as pandemic H1N1 as downloaded from the Influenza Virus Resource_ on September-5-2015.
plasmid_sequences_20150904.txt gives the sequences of the reverse genetics plasmids are provided by Hui-Ling Yen_ on September-4-2015.
.. Influenza Virus Resource: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
.. Hui-Ling Yen: http://sph.hku.hk/en/about-us/faculty-and-staff/academic-staff/yen,-hui-ling
.. Jesse Bloom: http://research.fhcrc.org/bloom/en.html
.. iPython notebook: http://ipython.org/notebook.html