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custom_analyses_data

README.md

Custom data

This subdirectory contains input data used by custom analyses jupyter notebooks and supplemental data for paper

Altair themes

theme.py:

  • File for setting custom altair themes, used by most notebooks for plotting

heatmap_theme.py:

  • File for setting custom altair themes, used by notebooks to make heatmaps

interactive_theme.py:

  • File for setting custom altair themes, used by notebooks to make large interactive figures

Paper Supplementary Data

./paper_supplementary_data:

  • Supplemental data for paper

Alignments and phylogenetics

/alignments:

  • ephrin_E2_E3_sequences.fasta Amino acid alignment of Human and Pteropus alecto EFNB2 and EFNB3
  • Nipah_RBP_AA_align.fasta Alignment of Nipah RBP sequences downloaded from GenBank
  • wild_type_seq.fasta wildtype sequence (non codon-optimized) of NiV-M RBP
  • Nipah-B_MK673572.1.fasta wildtype sequence of NiV-B RBP

/alignments/phylo:

  • country_genbank_ids.csv Country of origin of genbank sequences
  • nipah_whole_genome_alignment.fasta Alignment of whole genome nipah sequences
  • nipah_whole_genome_genbank_accession_ids.txt Accession IDs from genbank
  • nipah_whole_genome_phylo.tre Phylogeny of whole genome nipah sequences inferred from IQ-TREE

Protein crystal structures

/crystal_structures: PDB files of:

  • 2vsm.pdb (Nipah RBP bound to Ephrin-B2)
  • 3d12.pdb (Nipah RBP bound to Ephrin-B3)
  • 6cmg.pdb (Hendra RBP bound to m102.3)
  • 6vy4.pdb (Hendra RBP bound to HENV-32)
  • 6vy5.pdb (Nipah RBP bound to HENV-26)
  • 7txz.pdb (Partial Nipah RBP bound to nAH1.3)

Experimental data

/experimental_data: Raw experimental data of relative light units (RLUs) or fraction infectivity neutralization experiments. Also includes mAb, binding, and cell entry validation data. More information in readme in directory