Update October 28, 2000:
Added a Useful Links section at the bottom of the page. Currently it contains six GenBank links to VZV-MSP sequences from Charles Grose's lab.
Update October 20, 2000:
Multiple alignments added for ORFs 9, 10, 11, 17, 21, 22, 29, 31, 36, 37, 47, 48, 62. Graphics are shown under their respective ORF links. Structure analysis using Chou-Fasman is also up for ORF 62 for the Arvin Vaccine, Merck Vaccine, Yaminishi Vaccine, and Parental Oka (Yaminishi). In summary, no structural differences were encountered due to the two changes in the Arvin sequence. For best comparison, select the graphical squiggly plot in each and print out for comparison. More multiple alignments coming shortly!
Update September 25, 2000:
Added ORF locations table and noncoding region alignments for ORFs 14, 47&48, and 67. I was able to find ORF S/L for the P. Oka, but not in the Merck Vaccine. ORF S/L spans 125019 -> 837 in the P. Oka.
ORF 33 up. Has three amino acid differences, with two, two nucleotide differences. ORFs 42 and 45 are also up and are spliced together. No differences between either of them. That's it! All sequence alignments completed. It'll take about a day to clean-up the site, and fix up some things. Also, I'll have a summary table of differences and an ORF map up soon, which will be linked from this page.
ORFs 1-7, 30-37 added. 33, 42 and 45 coming tomorrow!
Wow! Summer's going by fast! ORF's 28-29, 51-52, 55-56 added. The rest coming soon! ORF 56 has a single amino acid insertion resulting from a 3 nt inerstion in the DNA sequence.
More ORFs added (38- 41, 43, 44, 46, 48, 49, 53, 54, 57-61). ORF 39 has a single nucleotide insertion resulting in an altered reading frame for the last ~35 amino acids at the C-terminal. ORF 51 also has a single nt insertion which changes the reading frame of the last ~90 amino acids, also at the C-terminal end. Both very interesting and noteworthy.
ORFs 8-27 finished. ORF 22 has a lot of variation with 11 amino acid differences.
Added ORF's 10 and 14. Some interesting results for 14, though I'm not sure if the deletions are correct upon examining the actual sequences by hand. Might be an error in the alignment program. 14's aligned two ways, first using Needleman-Wunzch which generated an inconsistency with the protein sequence alignment and then by Dot-Plot, which seemed consistent.
Added ORF's 63-70. Also put up a restriction enzyme site positions for BssHII and NaeI for ORF 62 as mentioned in the Gomi et. al. paper. for the Parent Oka, the Vaccine strain, and HEVZVXX.
ORF 4 sequence analysis is also up with 10, 14 and 61 on the way since those were shown to be relevant in the paper as well.
Web page is born! Alignment results will soon be posted in the left view bar by ORF number. Just click on the number to view a more detailed explanation. Discussion text box will be working soon with more alignments to come! Thanks and please send me any feedback!