Strain Alignment and Assembly Data
The sequences and annotations files in the table below represent the “trimmed” versions of the genomes. See Figure 1 for an explanation of how the genomes are trimmed. The full, untrimmed versions of each genome are found at Genbank, as well as in the zipped file below.
- HSV-1 Multi-Strain Alignment: HSV1_multi_genome_alignment_Szpara_Davison.fa
- HSV-1 GAP4 Output: HSV1_collection_GAP4_Szpara_Davison.zip
- All trimmed sequences and annotations: HSV1_trimmed_DNA_Szpara_Davison.zip
- All full length sequences and annotations: HSV1_collection_DNA_fullength_Szpara_Davison.zip
Amino Acid Conservation
- Amino Acid Alignments, unformatted (MSF multiple alignment format): AA_alignments_unformatted.zip
- Amino Acid Alignments, formatted into color coded PDF’s (split into groups for <50MB download size): UL1-UL14, UL15-UL26, UL27-UL36, UL37-UL49A, UL50-US12, RL1-RL2-RS1
- Positively selected residues (codeml output): Positive_selection_codeml_outputs.zip
- Positively selected residues (Slr output): Positive_selection_Slr_outputs.zip
Short Sequence Repeats
- Location and conservation of SSRs in 26 strains of HSV-1: Szpara_et_all_SSRs_26_HSV1_strains.xls
- Genome-browser compatible files to visualize SSRs and all other genome features of HSV-1 (Figure 3): Szpara_et_al_Figure3_files_for_genome_browser.zip
- Proportions of SSRs in genome regions, for all strains (Figure 4): Szpara_et_al_SSR_proportions_in_genome_regions.xls