Bioinformatics Lab 1

Part A - seq function

a: Create a vector where the first element is 1, the last element is 33, with an increment of 2 between elements.
b: Create a vector with 15 equally spaced elements in which the first element is 7 and the last element is 40.
c: Use the sample function to create a vector with variable name my.dna that consists of 20 uniformly-random letters “A”, “C”, “G”, and “T”.
d: Use the == logic operator and other R functions on your my.dna variable to determine how many of the letters are “A”. Hint: you can use sum on a TRUE/FALSE vector or you can use the functions which and length.
e: Confirm your answer in d with the table(my.dna). From the output of table, create a pie chart and barplot. Add x and y labels to your barplot.
f: Use the sample function with the option prob=c(.1,.4,.4,.1)to create a vector with variable name my.dna2 that consists of 20 non-uniformly random letters “A”, “C”, “G”, and “T”. Use table to show the nucleotide counts.

Part B: NCBI Search

Setup

Search NCBI (http://www.ncbi.nlm.nih.gov/) for “Alzheimer human.” This will take you to Entrez gene, which shows you the hits in the NCBI databases. Choose the top hit for Alzheimer under “Gene” information.

Evaluation

a: What is the name of the gene?
b: What chromosome is the gene on?
c: What species has the most similar gene to the human version?

Part C: Reading fasta files, nucleotide and dinucleotide frequencies

Setup

Install and load the seqnir library
Download the fasta file found from Part B
Read the fasta file in as a string

Evaluation

a: What data type is the fasta?
b: Create a function that converts the fasta string to a vector
c: Using the function from C.2, how long is the sequence?
d: Show the first 20 nucleotides of the sequence
e: How many of each nucleotide are there in the sequence?
f: Create a barplot of the counts, including axes labels
g: Calculate the probability of each nucleotide

Part D: GC Content

a: Add code to your R script to calculate the G+C content of the fasta vector
b: How many gc pairs are there?
c: Show a barplot of all dinucleotide counts

Part E: Coronavirus

Setup

Paper: https://www.ncbi.nlm.nih.gov/pubmed/32015508
DNA/RNA: https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3?report=fasta
Protein: https://www.ncbi.nlm.nih.gov/protein/QHD43415.1?report=fasta

Evaluation

a: Download the DNA/RNA fasta file and determine the nucleotide frequencies. Comment on how the frequencies compare with the human APOE gene.