Description

1.    What is meant by the term splicing, and how does this process contribute to the discrepancy between the relatively low number of genes in the human genome, but the larger number of proteins actually produced (over 100.000 proteins from only 20.000-22.000 genes) (3p)

For the tasks below, you need to spend time clicking around to explore the page(s) and find the info!

2.    In Ensembl (https://uswest.ensembl.org/index.html (Links to an external site.) ) (HUMAN GENOME) search for rs7412 by typing the variant name in the searching window! In which gene is this SNP found? (3p)

3.    Does it result in an amino acid exchange? If so, which one? (3p)

4.    What disease’s risk is increased by this variant? (3p)

5.    Go to uniport (https://www.uniprot.org (Links to an external site.) ) and make a fasta file with the gene protein products where rs7412 is located! Choose the first 5 species in the table! (18p (9p-9p))

Save as a txt file! Change the extension txt to fasta!

Used the code below to build a phylogenetic tree!

Bioconductor https://www.bioconductor.org (Links to an external site.)

Install the packages if I have not done yet!

Call them in by library()

if (!requireNamespace("BiocManager", quietly=TRUE))

    install.packages("BiocManager")

BiocManager::install("msa")

library(msa)

library(ape)

library(ggtree)

library(ggplot2)

library(seqinr)

https://bioconductor.org/packages/release/bioc/vignettes/msa/inst/doc/msa.pdf (Links to an external site.)

Importing the file into R

First, set the directory in R (where your fasta file is located)

Check the path with code: getwd()

File Import code:

mySequences <- readAAStringSet(filepath = "/Users/anitalakatos/Desktop/myfastafile.fasta", format = "fasta")

myFirstAlignment <- msa(mySequences,method = "ClustalW",cluster ="upgma",substitutionMatrix = "blosum",type = "protein")

print(myFirstAlignment, show="complete")

msaPrettyPrint(myFirstAlignment, output="pdf", showNames="left",

               showLogo="none", askForOverwrite=FALSE, verbose=FALSE)

*the file myFirstAlignment.tex  is saved in your directory, you can open it with a text editor

 myFirstAlignment.tex  (TextShop  on Mac, or the LATEX package TEXshade,

TeXworks for both Mac and Windows)

Please paste the figure!!!!!!!!!!

myFirstAlignment_2 <- msaConvert(myFirstAlignment_2, type="seqinr::alignment")

d <- dist.alignment(myFirstAlignment_2, "identity")

library(ape)

myTree <- nj(d)

plot(myTree, main="Phylogenetic Tree of  ")

class(myTree)

ggtree(myTree, color="firebrick", size=1) + geom_tiplab(color="blue", size=3) +

geom_treescale(x=1, y=1,offset = 0,width = 0)

Please paste the figure!!!!!!!!!