Wed. Feb 5, 2019, Oyster Seed Proteomics Uniprot and Network Mapping

remapping proteins sequences to 2019 Uniprot DB

reference this jupyter notebook: 20190130_Cg_Giga_cont_AA.fa_BLASTP_uniprot_swprot2019.ipynb

  1. Rebuilt the BLAST index from 2019 Uniprot DB
  2. remapped protein sequences from Steven’s file http://gannet.fish.washington.edu/halfshell/bu-git-repos/nb-2017/C_gigas/data/Cg_Giga_cont_AA.fa to updated Uniprot DB.

  3. reformatted BLAST output to remove pipes in protein names and contain the following fields:

fold change analysis and p-value

  • made all fold change comparisons for all time points and temperatures to time 0, and calculated p-values using chi square proportions test. Did not do anything with zero values.
Written on February 5, 2019