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Contents 1 2011 2 Schedule 3 ADDA algorithm 3.1 How to get residue correlation matrix

2011

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1. Error fetching PMID 12706730: [ADDA]

Schedule

ADDA algorithm

How to get residue correlation matrix

# set working directory
setwd("/Users/igchoi/Downloads/")
# read blast table
tmp = read.table("sample.tab",sep="\t")
# dimension
dim(tmp)
# extract gi number
tmp[,1] = sapply(as.vector(tmp[,1]), function(x) {
  y = strsplit(x,"\\|"); return(unlist(y)[2]) })
tmp[,2] = sapply(as.vector(tmp[,2]), function(x) {
  y = strsplit(x,"\\|"); return(unlist(y)[2]) })
#
tmp[1:5,]
# V7-V8 V9-V10 (aligned?)
# query = 590 residues
count.que = matrix(0,nrow(tmp),590)
for(i in 1:nrow(tmp)) {
  res = unlist(tmp[i,7:8])
  print(res)
  count.que[i,c(res[1]:res[2])] = 1
}
image(t(count.que),col=c("white","blue"))
# count number of neighbors occurring both position i and j
corr = matrix(0,590,590)
for (i in 1:ncol(count.que)) {
  for (j in i:ncol(count.que)) {
    print(paste(i,j))
    chk = count.que[,i]+count.que[,j]
    cnt = length(which(chk==2))
    corr[i,j] = cnt
  }
}
range(corr)
image(corr,col=topo.colors(10))