reference_sequences

Reference sequences

This subdirectory contains contains SARS-CoV-2 spike reference sequences and lookup tables required to renumber positions between variants.

Files

• pH2rU3_ForInd_sinobiological_617.2_Spiked21_CMV_ZsGT2APurR.gb genbank file for plasmid used to generate spike DMS library

• B16172_extended_ends_for_primers.txt Delta variant spike sequence containing flanking plasmid sequences, copied from pH2rU3_ForInd_sinobiological_617.2_Spiked21_CMV_ZsGT2APurR.gb plasmid. Used in generating DMS primers.

• B16172_extended_ends_for_paired_primers.fasta fasta file of Delta variant spike sequence containing plasmid sequences, copied from pH2rU3_ForInd_sinobiological_617.2_Spiked21_CMV_ZsGT2APurR.gb plasmid. Used in generating paired DMS primers.

• homo_codon_freq_del.csv Human codon frequencies used in DMS primer design. Frequencies were obtained from here

• reference_sequence_position_lookup.csv table used to look up SARS-CoV-2 variant spike sequence positions in relation to Wuhan-1 spike sequence. Columns are as follows:

  • parent_seq Wuhan-1 spike amino acid sequence
  • variant_seq Delta variant spike amino acid sequence
  • parent_pos Wuhan-1 spike amino acid position
  • variant_pos Delta variant spike amino acid position
  • variant_sig Signiture amino acid changes in Delta variant. Yes for amino acid changes that are unique to Delta variant and No for amino acids that are the the same in relation to Wuhan-1 sequence.