bch441-work-abc-units/BIN-ALI-Similarity.R

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# tocID <- "BIN-ALI-Similarity.R"
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Similarity unit.
#
# Version: 1.2
#
# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 2020 Updates
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout
# 1.0 Refactored for 2017; add aaindex, ternary plot.
# 0.1 First code copied from 2016 material.
#
#
# TODO:
# Update ggtern:: ternary plot to use aacol dots under text
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
#
# If there are portions you don't understand, use R's help system, Google for an
# answer, or ask your instructor. Don't continue if you don't understand what's
# going on. That's not how it works ...
#
# ==============================================================================
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ----------------------------------------------
#TOC> 1 Amino Acid Properties 43
#TOC> 2 Mutation Data matrix 189
#TOC> 3 Background score 230
#TOC>
#TOC> ==========================================================================
# = 1 Amino Acid Properties ===============================================
# A large collection of amino acid property tables is available via the seqinr
# package:
if (! requireNamespace("seqinr", quietly=TRUE)) {
install.packages("seqinr")
}
# Package information:
# library(help = seqinr) # basic information
# browseVignettes("seqinr") # available vignettes
# data(package = "seqinr") # available datasets
# A true Labor of Love has gone into the compilation of the seqinr "aaindex"
# data:
?aaindex
data(aaindex, package = "seqinr") # load the aaindex list from the package
length(aaindex)
# Here are all the index descriptions
for (i in 1:length(aaindex)) {
cat(paste(i, ": ", aaindex[[i]]$D, "\n", sep=""))
}
# It's a bit cumbersome to search through the descriptions ... here is a
# function to make this easier:
searchAAindex <- function(patt) {
# Searches the aaindex descriptions for regular expression "patt"
# and prints index number and description.
hits <- which(sapply(aaindex, function(x) length(grep(patt, x$D)) > 0))
for (i in seq_along(hits)) {
cat(sprintf("%3d\t%s\n", hits[i], aaindex[[ hits[i] ]]$D))
}
}
searchAAindex("free energy") # Search for "free energy"
searchAAindex("(size)|(volume)") # Search for "size" or "volume":
# Let's examine ...
# ... a hydrophobicity index
(Y <- aaindex[[528]][c("D", "I")])
# ... a volume index
(V <- aaindex[[150]][c("D", "I")])
# ... and one of our own: side-chain pK values as reported by
# Pace et al. (2009) JBC 284:13285-13289, with non-ionizable pKs set
# to 7.4 (physiological pH)
K <- list(I = c( 7.4, # Ala
12.3, # Arg
7.4, # Asn
3.9, # Asp
8.6, # Cys
7.4, # Gln
4.3, # Glu
7.4, # Gly
6.5, # His
7.4, # Ile
7.4, # Leu
10.4, # Lys
7.4, # Met
7.4, # Phe
7.4, # Pro
7.4, # Ser
7.4, # Thr
7.4, # Trp
9.8, # Tyr
7.4)) # Val
names(K$I) <- c("Ala","Arg","Asn","Asp","Cys","Gln","Glu","Gly","His","Ile",
"Leu","Lys","Met","Phe","Pro","Ser","Thr","Trp","Tyr","Val")
# Given these biophysical indices, how similar are the amino acids? We have three-dimensions of measures here. Scatterplots can only display two dimensions ...
# pull the names from Y$I, convert them to single letter code, and reorder the
# AACOLS palette accordingly ...
aac <- AACOLS[toupper(seqinr::a(names(Y$I)))]
plot(Y$I, V$I,
xlab = "hydrophobicity", ylab = "volume",
pch = 21,
cex = 6,
col = aac,
bg = aac)
text(Y$I, V$I, names(Y$I), cex = 0.8)
plot(Y$I, K$I,
xlab = "hydrophobicity", ylab = "pK",
pch = 21,
cex = 6,
col = aac,
bg = aac)
text(Y$I, K$I, names(Y$I), cex = 0.8)
# ... but how do we plot 3D data? Plotting into a 3D cube is possible, but such
# plots are in general unintuitive and hard to interpret. One alternative is a
# so-called "ternary plot":
if (! requireNamespace("ggtern", quietly=TRUE)) {
install.packages("ggtern")
}
# Package information:
# library(help = ggtern) # basic information
# browseVignettes("ggtern") # available vignettes
# data(package = "ggtern") # available datasets
# collect into data frame, normalize to (0.05, 0.95)
myDat <- data.frame("phi" = 0.9*(((Y$I-min(Y$I))/(max(Y$I)-min(Y$I))))+0.05,
"vol" = 0.9*(((V$I-min(V$I))/(max(V$I)-min(V$I))))+0.05,
"pK" = 0.9*(((K$I-min(K$I))/(max(K$I)-min(K$I))))+0.05,
stringsAsFactors = FALSE)
rownames(myDat) <- names(Y$I)
ggtern::ggtern(data = myDat,
ggplot2::aes(x = vol,
y = phi,
z = pK,
label = rownames(myDat))) + ggplot2::geom_text()
# This results in a mapping of amino acids relative to each other that is
# similar to the Venn diagram you have seen in the notes.
# ... or we could use principal components analysis, to pull out the
# best projection of the three feature dimensions into two. (Done here without delving
# into the theory ...)
prc <- prcomp(myDat)
plot(prc$x[,1], prc$x[,2], xlab="", ylab="", xaxt="n", yaxt="n",
pch=19, cex=6, col=aad, cex.main=0.7,
main="Principal Component Analysis of Amino Acid Features")
text(prc$x[,1], prc$x[,2], names(Y$I), cex = 0.8, col="#00000088")
# This matches the intuition rather well in that "similar" amino acids are close
# on the plot. But we can't interpret the distances in terms of just one of the
# parameters. Whatever - nature has a different way to define similarity:
# mutations to similar amino acids are less likely to break the protein.
# = 2 Mutation Data matrix ================================================
# A mutation data matrix encodes all amino acid pairscores in a matrix.
# The Biostrings package contains the most common mutation data matrices.
if (! requireNamespace("BiocManager", quietly=TRUE)) {
install.packages("BiocManager")
}
if (! requireNamespace("Biostrings", quietly=TRUE)) {
BiocManager::install("Biostrings")
}
# Package information:
# library(help=Biostrings) # basic information
# browseVignettes("Biostrings") # available vignettes
# data(package = "Biostrings") # available datasets
# Let's attach the BLOSUM62 mutation data matrix from the package
data(BLOSUM62, package = "Biostrings")
# ... and see what it contains. (You've seen this matrix before.)
BLOSUM62
# We can simply access values via the row/column names.
# Identical amino acids have high scores ...
BLOSUM62["H", "H"] # Score for a pair of two histidines
BLOSUM62["S", "S"] # Score for a pair of two serines
# Similar amino acids have low positive scores ...
BLOSUM62["L", "I"] # Score for a leucine / lysine pair
BLOSUM62["F", "Y"] # etc.
# Dissimilar amino acids have negative scores ...
BLOSUM62["L", "K"] # Score for a leucine / lysine pair
BLOSUM62["Q", "P"] # etc.
BLOSUM62["R", "W"] # the matrix is symmetric!
BLOSUM62["W", "R"]
# = 3 Background score ====================================================
# The mutation data matrix is designed to give high scores to homologous
# sequences, low scores to non-homologous sequences. What score on average
# should we expect for a random sequence?
# If we sample amino acid pairs at random, we will get a score that is the
# average of the individual pairscores in the matrix. Omitting the ambiguity
# codes and the gap character:
sum(BLOSUM62[1:20, 1:20])/400
# But that score could be higher for real sequences, for which the amino acid
# distribution is not random. For example membrane proteins have a large number
# of hydrophobic residues - an alignment of unrelated proteins might produce
# positive scores. And there are other proteins with biased amino acid
# compositions, in particular poteins that interact with multiple other
# proteins. Let's test how this impacts the background score by comparing a
# sequence with shuffled sequences. These have the same composition, but are
# obvioulsy not homologous. The data directory contains the FASTA file for the
# PDB ID 3FG7 - a villin headpiece structure with a large amount of
# low-complexity amino acid sequence ...
aa3FG7 <- Biostrings::readAAStringSet("./data/3FG7.fa")[[1]]
# ... and the FASTA file for the E. coli OmpG outer membrane porin (PDB: 2F1C)
# with an exceptionally high percentage of hydrophobic residues.
aa2F1C <- Biostrings::readAAStringSet("./data/2F1C.fa")[[1]]
# Here is a function that takes two sequences and
# returns their average pairscore.
averagePairScore <- function(a, b, MDM = BLOSUM62) {
# Returns average pairscore of two sequences.
# Parameters:
# a, b chr amino acid sequence string
# MDM mutation data matrix. Default is BLOSUM62
# Value: num average pairscore.
a <- unlist(strsplit(a, ""))
b <- unlist(strsplit(b, ""))
v <- 0
for (i in seq_along(a)) {
v <- v + MDM[ a[i], b[i] ]
}
return(v / length(a))
}
orig3FG7 <- toString(aa3FG7)
orig2F1C <- toString(aa2F1C)
N <- 1000
scores3FG7 <- numeric(N)
scores2F1C <- numeric(N)
for (i in 1:N) {
scores3FG7[i] <- averagePairScore(orig3FG7, toString(sample(aa3FG7)))
scores2F1C[i] <- averagePairScore(orig2F1C, toString(sample(aa2F1C)))
}
# Plot the distributions
hist(scores3FG7,
col="#5599EE33",
breaks = seq(-1.5, 0, by=0.1),
main = "Pairscores for randomly shuffled sequences",
xlab = "Average pairscore from BLOSUM 62")
hist(scores2F1C,
col="#55EE9933",
breaks = seq(-1.5, 0, by=0.1),
add = TRUE)
abline(v = sum(BLOSUM62[1:20, 1:20])/400, col = "firebrick", lwd = 2)
legend('topright',
c("3FG7 (villin)", "2F1C (OmpG)"),
fill = c("#5599EE33", "#55EE9933"), bty = 'n',
inset = 0.1)
# This is an important result: even though we have shuffled significantly biased
# sequences, and the average scores trend above the average of the mutation data
# matrix, the average scores still remain comfortably below zero. This means
# that we can't (in general) improve a high-scoring alignment by simply
# extending it with randomly matched residues. We will only improve the score if
# the similarity of newly added residues is larger than what we expect to get by
# random chance!
# [END]