data

Input data

This directory contains input data used for the analysis and configuration for some of the analyses:

• barcode_runs.csv: Illumina sequencing runs for barcode counting. The sample column should be the hyphen separated concatenation of experiment, antibody, concentration, and selection. The combination of the library and sample columns should be unique. The frac_escape column gives the overall fraction of the library that escaped antibody. The R1 FASTQ files should be semicolon (; ) separated list of glob patterns.

• wildtype_sequence.fasta: wildtype sequence of mutagenized gene.

• ./pdbs/: files downloaded from the Protein Data Bank for structural analyses. The 7c01.pdb structure was modified to give the 7c01_single.pdb: the original structure has two Fab:RBD complexes within the asymmetric unit, so we removed chains B, C, and D to leave just one complex for visualization.

• escape_profiles_config.yaml: Information on how to plot the escape profiles; manually edit this to alter their plotting.

• mds_config.yaml: Information on how to do the multi-dimensional scaling.

• output_pdbs_config.yaml: Information on how to output structural mappings of escape.

• structural_annotation_config.yaml: Information on how to output structural annotations of contact residues in various RBD:ligand complexes.

• site_color_schemes.csv: Schemes for how to color sites (can be used in escape profiles). Here are details on these schemes.

  • The subdomain scheme colors sites orange if they directly contact ACE2 (within 4 angstroms in PDB 6m0j) in the SARS-CoV-2 structure (residues 417, 446, 449, 453, 455, 456, 475, 486, 487, 489, 493, 496, 498, 500, 501, 502, 505), blue if they are in the receptor binding motif (RBM, residue 437 to 508, inclusive), and green if they are in the core RBD domain (all other sites). These definitions match those used in Starr et al (2020).

• ./RBD_sites.csv: Useful numeric and functional annotations of RBD sites for referencing in various analyses.

• ./RBDs_aligned.fasta: alignment of sarbecovirus RBDs

• escape_selection_results.yaml: results of viral escape-mutant selections, used to make plots about these.

• Whelan-VSV-SARS-CoV-2-Spike.gb is the sequence of the Spike in the VSV virus expressing the SARS-CoV-2 Spike used by the Crowe lab (originally from Whelan lab); sequence provided by Seth Zost.

• ./pse_config.yaml: config file for writing pymol commands to create a PSE session for certain selections.