# 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. Hint: use ?seq for help and the option length.out option.

### 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. 

### 1. What is the name of the gene?

### 2. What chromosome is the gene on?

### 3. 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

### 1. What data type is the fasta?

### 2. Create a function that converts the fasta string to a vector

### 3. Using the function from C.2, how long is the sequence?

### 4. Show the first 20 nucleotides of the sequence

### 5. How many of each nucleotide are there in the sequence?

### 6. Create a barplot of the counts, including axes labels

### 7. Calculate the probability of each nucleotide

## Part D: GC Content

### 1. Add code to your R script to calculate the G+C content of the fasta vector

### 2. How many gc pairs are there?

### 3. 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  


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