{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":146521105,"defaultBranch":"master","name":"zika-tutorial","ownerLogin":"nextstrain","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2018-08-29T00:10:54.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/22159334?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1694769752.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"82c06bb002c509f0e512aef79c6eeed64a03efae","ref":"refs/heads/add-default-profile","pushedAt":"2023-09-15T09:22:32.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"corneliusroemer","name":"Cornelius Roemer","path":"/corneliusroemer","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/25161793?s=80&v=4"},"commit":{"message":"Add default profile to set Snakemake CLI args\n\nThe special profile at `profiles/default/config.yaml` is used by snakemake >= 7.29\nby default without requiring passing in via\n`--profile profiles/default`\n\nProfiles are nice because they reduce number of CLI args\nrequired when invoking `snakemake`","shortMessageHtmlLink":"Add default profile to set Snakemake CLI args"}},{"before":null,"after":"75eb166ca95079a25049c421613081c575c2f09d","ref":"refs/heads/annotation-updates","pushedAt":"2023-08-18T00:26:23.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"jameshadfield","name":"james hadfield","path":"/jameshadfield","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/8350992?s=80&v=4"},"commit":{"message":"Add prM protein, remove PRO (pr) protein\n\nThe precursor protein is cleaved into ~10 proteins including the\nprecusor membrane protein (prM). prM is subsequently cleaved by the host\nprotease furin resulting in protein M (aka MP).\n\nThe previous annotation included CDSs PRO and MP, but not the (parent)\nprM protein. prM is cleaved directly from the polyprotein and is\nfunctional, forming heterodimers with protein E (similar behaviour\nacross all flaviviruses I believe).\n\nNCBI's genome viewer shows both prM as well as both the sub-proteins\nafter cleavage, pr and M. pr would correspond to the previous PRO\nannotation. I've not seen protein pr referenced anywhere else so I've not\nincluded that here.\n\nNote that this change wasn't desirable before Auspice could display\noverlapping CDSs <https://github.com/nextstrain/auspice/pull/1684>.\n\nReferences:\n<https://www.microbiologyresearch.org/content/journal/jgv/10.1099/vir.0.18723-0>\n<https://www.ncbi.nlm.nih.gov/gene/7751225>","shortMessageHtmlLink":"Add prM protein, remove PRO (pr) protein"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAADgUzp3QA","startCursor":null,"endCursor":null}},"title":"Activity · nextstrain/zika-tutorial"}