2d:null 2e:["$","title",null,{"children":"difCGR | deAlmeida | Observable"}] 33:[] 31:{"id":"d48623a8ee34385b","slug":"difcgr","title":"difCGR","thumbnail":"621147633a5e503f3135735e34d7308260c087c691fdc6f9cf03dfee483309ef","access_level":"public","create_time":"$D2025-07-14T15:00:07.898Z","update_time":"$D2025-07-16T15:20:42.040Z","view_time":null,"first_public_time":"$D2025-07-14T15:00:56.440Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"14afccedf51bc3cf","login":"dealmeida","name":"deAlmeida","avatar_url":"https://avatars-next.observableusercontent.com/6f2483a702e72919a51bbe6b8e0f039682966ee32dc2dbb79f9f4faa40f6431d","tier":"starter_2024"},"version":301,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"32cd85513d6a9710","login":"almeidajonas","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/993b061f7ee4ef1ccb82cfd216deb36c6e58eac2103450d2ccecc03281c2411e","tier":null}],"members":[{"type":"individual","id":"32cd85513d6a9710","login":"almeidajonas","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/993b061f7ee4ef1ccb82cfd216deb36c6e58eac2103450d2ccecc03281c2411e","tier":null,"role":"editor"},{"type":"team","id":"14afccedf51bc3cf","login":"dealmeida","name":"deAlmeida","avatar_url":"https://avatars-next.observableusercontent.com/6f2483a702e72919a51bbe6b8e0f039682966ee32dc2dbb79f9f4faa40f6431d","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"difCGR","cells":[{"id":0,"value":"# difCGR\n

USM ^{[code][YouTube]}

\n\n

Extracting a SNP signal by subtraction of the respectiveUSMs

\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":15,"value":"### Load USM module","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":13,"value":"usm = require(\"https://usm.github.io/2/usm2.js\")","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"## load reference EGFR sequence (EGFR, L = 244589)","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":21,"value":"egfrSeq0 = usm.resolveSeq(\n \"https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=399923581&db=nuccore&report=fasta&extrafeat=null&conwithfeat=on&hide-cdd=on&retmode=html&withmarkup=on&tool=portal&log$=seqview\"\n)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":23,"value":"seq0=egfrSeq0.seq","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"## insert mutation, pos 100, \"A\" > \"G\"","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":57,"value":"seq0.slice(100,101)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":227,"value":"seq0.length","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":97,"value":"seq1 = [seq0.slice(0,100),\"G\",seq0.slice(101)].join('')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":225,"value":"seq1.length","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":241,"value":"[seq0.slice(98,103),seq1.slice(98,103)]","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":105,"value":"## extract signal from noise","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":102,"value":"u0 = new usm(seq0)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":107,"value":"u1=new usm(seq1)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":109,"value":"## generate respective FCGRs","pinned":true,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":183,"value":"k=2","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":112,"value":"fcgr0=u0.fcgr(k)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":115,"value":"u0.plotCanvas(k,'forward')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":126,"value":"fcgr1 = u1.fcgr(k)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":128,"value":"u0.plotCanvas(k,'backward')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":134,"value":"## Subtract FCGR","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":211,"value":"sub01 = fcgr0.map((row,i)=>row.map((c,j)=>(c-fcgr1[i][j])))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 32:"$31:body"

USM [code][YouTube]

USM ^{[code][YouTube]}