From c9285e74e472efa9f40181e99dfa1e5cfdc0e649 Mon Sep 17 00:00:00 2001 From: noah Date: Tue, 30 Aug 2022 15:01:24 -0500 Subject: [PATCH] README formatting --- README.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 94f1637..a04e870 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,12 @@ ## 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. +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 @@ -17,9 +17,9 @@ Search NCBI (http://www.ncbi.nlm.nih.gov/) for “Alzheimer human.” This will ### 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? +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 @@ -31,19 +31,19 @@ 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 +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 +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 @@ -53,5 +53,5 @@ 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. +a) Download the DNA/RNA fasta file and determine the nucleotide frequencies. Comment on how the frequencies compare with the human APOE gene.