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hivdb / covid-drdb

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Omicron alignment issue #16

Closed KaimingTao closed 2 years ago

KaimingTao commented 2 years ago

Spike NTD position 212 to 215, example: hCoV-19/Germany/HE-FFM-30286807/2021|EPI_ISL_6959871|2021-11-28

philiptzou commented 2 years ago

The issue is caused by codon-alignment process done by hivdb/post-align. In nutshell, position 212 and 214 (not 215!) are too close and the codon-alignment process considers them a single gap but not two.

The solution is a simple alignment profile change, which applies codon alignment to S:1-213 (in nucleotide: 21563-22201) and S:214-1274 (in nucleotide: 22202-25384) separately. This change allows the two gaps won't be merged as a single one. It has been added by hivdb/sierra-sars2@7a768a3.

Attachments:

  1. Before the change, the result: Screen Shot 2022-01-16 at 5 40 54 PM
  2. After the change, the result: Screen Shot 2022-01-16 at 5 36 29 PM