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Finalizing primary structure and DNA palindromes

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Noah L. Schrick 2022-10-27 15:22:11 -05:00
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1,2)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.breaks[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1,2,3)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.breaks[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.breaks[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
#g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.breaks <- g.hist$breaks # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.breaks[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
alpha.LM
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=5)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2, lwd=3)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
#plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3, lwd=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4, lwd=3)
plot(yeast)
hist(yeast)
hist(g.vec)
g.pois
g.mean
alpha.LM
alpha.ML
degree(g)
sort(degree(g))
sort(degree(g),decreasing=FALSE)
sort(degree(g),decreasing=F)
sort(degree(g),decreasing=false)
sort(degree(g), decreasing = TRUE)
head(sort(degree(g), decreasing = TRUE))
stddev(degree(g))
sd(degree(g))
tail(sort(degree(g), decreasing = TRUE))
plot(log(g.breaks.clean), log(g.probs.clean))
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
# Degree Distribution
# Professor: Dr. McKinney, Spring 2022
# Noah Schrick - 1492657
library(igraph)
library(igraphdata)
data(yeast)
g <- yeast
g.netname <- "Yeast"
################# Set up Work #################
g.vec <- degree(g)
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
" Network"))
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
"#006CD1", "#E66100", "#D35FB7"))
g.mean <- mean(g.vec)
g.seq <- 0:max(g.vec) # x-axis
################# Guessing Alpha #################
alpha.guess <- 1.5
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
################# Poisson #################
g.pois <- dpois(g.seq, g.mean, log=F)
lines(g.seq, g.pois, col="#006CD1", lty=2, lwd=3)
################# Linear model: Least-Squares Fit #################
g.breaks <- g.hist$breaks[-c(1)] # remove 0
g.probs <- g.hist$density[-1] # make lengths match
# Need to clean up probabilities that are 0
nz.probs.mask <- g.probs!=0
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
plot(log(g.breaks.clean), log(g.probs.clean))
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
summary(g.fit)
alpha.LM <- coef(g.fit)[2]
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3, lwd=3)
################# Max-Log-Likelihood #################
n <- length(g.breaks.clean)
kmin <- g.breaks.clean[1]
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
alpha.ML
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4, lwd=3)
plot(log(g.breaks.clean), log(g.probs.clean))
g.breaks.clean <- g.breaks[nz.probs.mask]
g.probs.clean <- g.probs[nz.probs.mask]
plot(log(g.breaks.clean), log(g.probs.clean))
# Lab 7 for the University of Tulsa's CS-6643 Bioinformatics Course
# PDB
# Professor: Dr. McKinney, Fall 2022
# Noah L. Schrick - 1492657
## Set Working Directory to file directory - RStudio approach
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
#### Part A: Obtaining PDB - no supporting R Code
#### Part B: Visualize the 3D structure
## Install Rpdb and load the pdb
if (!require("Rpdb")) install.packages("Rpdb")
library(Rpdb)
x<-read.pdb("1TGH.pdb")
## Visualize the B and C chains
B_chain_pdb <- subset(x$atoms, x$atoms$chainid=="B")
# Lab 7 for the University of Tulsa's CS-6643 Bioinformatics Course
# PDB
# Professor: Dr. McKinney, Fall 2022
# Noah L. Schrick - 1492657
## Set Working Directory to file directory - RStudio approach
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
#### Part A: Obtaining PDB - no supporting R Code
#### Part B: Visualize the 3D structure
## Install Rpdb and load the pdb
if (!require("Rpdb")) install.packages("Rpdb")
library(Rpdb)
x<-read.pdb("1TGH.pdb")
natom(x)
visualize(x,type="l")
## Visualize the B and C chains
B_chain_pdb <- subset(x$atoms, x$atoms$chainid=="B")
C_chain_pdb <- subset(x$atoms, x$atoms$chainid=="C")
# remove water:
C_chain_pdb <- subset(C_chain_pdb,C_chain_pdb$resname!="HOH")
# visualize chains B and C
BC_chains_pdb <- subset(x$atoms, x$atoms$chainid=="B" | x$atoms$chainid=="C")
color.vec <- c(rep("red",natom(B_chain_pdb)),rep("green",natom(C_chain_pdb)))
visualize(BC_chains_pdb,col=color.vec)
addResLab(BC_chains_pdb)
rgl.postscript("BC_chains.pdf","pdf",drawText=TRUE)
## Visualize B-C and A Chains
A_chain_pdb <- subset(x$atoms, x$atoms$chainid=="A")
# remove water
A_chain_pdb <- subset(A_chain_pdb, A_chain_pdb$resname!="HOH")
# visualize complex complex
BCA_chains_pdb <- subset(x$atoms, x$atoms$chainid=="B" |
x$atoms$chainid=="C" | x$atoms$chainid=="A")
BCA.color.vec <- c(rep("red",natom(B_chain_pdb)),rep("green",natom(C_chain_pdb)),rep("blue",natom(A_chain_pdb)))
visualize(BCA_chains_pdb,col=BCA.color.vec)
rgl.postscript("full_complex.pdf","pdf",drawText=TRUE)
# get coordinates of C1' atoms of the C-chain DNA molecule
C_chain_pdb$resname
C_chain_resids<-unique(C_chain_pdb$resid)
C_chain_C1prime <- subset(C_chain_pdb, C_chain_pdb$elename=="C1'")
# get chain C DNA sequence
C_chain_sequence_messy <- C_chain_C1prime$resname
C_chain_sequence <- paste(sapply(C_chain_sequence_messy,function(x) {unlist(strsplit(x,""))[2]}),collapse = "")
C_chain_sequence_messy
C_chain_sequence

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.~lock.pdb_lab.docx#
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@ -1 +1 @@
,noah,NovaArchSys,27.10.2022 13:09,file:///home/noah/.config/libreoffice/4;
,noah,NovaArchSys,27.10.2022 15:21,file:///home/noah/.config/libreoffice/4;

21
Schrick-Noah_CS-6643_Lab7.R
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@ -40,3 +40,24 @@ BCA_chains_pdb <- subset(x$atoms, x$atoms$chainid=="B" |
BCA.color.vec <- c(rep("red",natom(B_chain_pdb)),rep("green",natom(C_chain_pdb)),rep("blue",natom(A_chain_pdb)))
visualize(BCA_chains_pdb,col=BCA.color.vec)
#### Part C: Primary structure and DNA Palindromes
# get coordinates of C1' atoms of the C-chain DNA molecule
C_chain_pdb$resname
C_chain_resids<-unique(C_chain_pdb$resid)
C_chain_C1prime <- subset(C_chain_pdb, C_chain_pdb$elename=="C1'")
# get chain C DNA sequence
C_chain_sequence_messy <- C_chain_C1prime$resname
C_chain_sequence <- paste(sapply(C_chain_sequence_messy,function(x) {unlist(strsplit(x,""))[2]}),collapse = "")
## Find palindromes
if (!require("BiocManager")) install.packages("BiocManager")
library(BiocManager)
if (!require("Biostrings")) BiocManager::install("Biostrings")
library(snpStats)
C_chain_DNAString <- DNAString(C_chain_sequence)
dna.pals <- findPalindromes(C_chain_DNAString, min.armlength=3,
max.looplength=5, max.mismatch = 0)

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pdb_lab.docx
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