Scripts for reproducing TLR4 zebrafish analysis

Results of analysis reported in:

Loes AN, Hinman MN, Farnsworth DR, Miller AC, Guillemin K, Harms MJ Identification and characterization of zebrafish Tlr4 co-receptor Md-2 https://www.biorxiv.org/content/10.1101/817528v1

Prerequisites:

• binaries
  • makeblastdb
• python libraries
  • numpy
  • scipy
  • pandas
  • jupyter
  • phylopandas
  • phylogenetics
  • descartes
  • shapely

Run in the following order

• 00_run-me.sh: download relevant genomes from NCBI and convert to blast databases.
• 01_blast-genomes.ipynb: BLAST all genomes with regions surrounding human and zebraafish TLR4
• 02_characterize-genomic-context.ipynb: Generate plots of hit vs. genome position

Files related to analysis:

• files/md1-and-md2.csv: Spreadsheet containing accession numbers and aligned sequences for Md-1 and Md-2 phylogenetics.
• files/cd180-and-tlr4.csv: Spreadsheet containing accession numbers and aligned sequences for CD180 and TLR4 phylogenetics.
• files/ly96-gene-locations.xlsx: Gene locations for ly96 synteny analysis
• files/genomes-for-tlr4-synteny.xlsx: Genomes used for tlr4 synteny analysis
• files/human-and-tlr4-genes.xlsx: Genes used to BLAST for human vs. zebrafish Tlr4 genomic context
• synteny-results/: PDF files showing running average of e-value along genomes