86 lines
2.7 KiB
Markdown
86 lines
2.7 KiB
Markdown
# Bioinformatics Lab 1
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## Part A - seq function
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### a:
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Create a vector where the first element is 1, the last element is 33, with an increment of 2 between elements.
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### b:
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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.
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### c:
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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”.
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###d:
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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.
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### e:
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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.
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### f:
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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.
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## Part B: NCBI Search
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### Setup:
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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.
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### 1.
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What is the name of the gene?
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### 2.
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What chromosome is the gene on?
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### 3.
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What species has the most similar gene to the human version?
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## Part C: Reading fasta files, nucleotide and dinucleotide frequencies
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### Setup:
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Install and load the seqnir library
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Download the fasta file found from Part B
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Read the fasta file in as a string
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### 1.
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What data type is the fasta?
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### 2.
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Create a function that converts the fasta string to a vector
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### 3.
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Using the function from C.2, how long is the sequence?
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### 4.
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Show the first 20 nucleotides of the sequence
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### 5.
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How many of each nucleotide are there in the sequence?
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### 6.
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Create a barplot of the counts, including axes labels
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### 7.
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Calculate the probability of each nucleotide
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## Part D: GC Content
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### 1.
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Add code to your R script to calculate the G+C content of the fasta vector
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### 2.
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How many gc pairs are there?
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### 3.
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Show a barplot of all dinucleotide counts
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## Part E: Coronavirus
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### Setup
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Paper: https://www.ncbi.nlm.nih.gov/pubmed/32015508
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DNA/RNA: https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3?report=fasta
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Protein: https://www.ncbi.nlm.nih.gov/protein/QHD43415.1?report=fasta
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### 1.
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Download the DNA/RNA fasta file and determine the nucleotide frequencies. Comment on how the frequencies compare with the human APOE gene.
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