Manipulate Biological Data Using Biostrings Package Exercises(Part 2)

May 28, 2017
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(This article was first published on R-exercises, and kindly contributed to R-bloggers)


Bioinformatics is an amalgamation Biology and Computer science.Biological Data is manipulated using Computers and Computer software’s in Bioinformatics. Biological Data includes DNA; RNA & Proteins. DNA & RNA is made of Nucleotide which are our genetic material in which we are coded.Our Structure and Functions are done by protein, which are build of Amino acids

In this exercise we try correlate the relation between DNA, RNA & Protein.

Conversion of DNA to RNA is known as Transcription. DNA/RNA to protein is known as Translation.

Here we also discuss Sequence Alignment Techniques. Sequence Alignment is comparing the similarity between the sequences to check how much the DNA,RNA or Protein are related to each other.
Three are three types of Sequence Alignment
1. Global Alignment
2. Local Alignment
3. Over lap Alignment

In the exercises below we cover how we can Manipulate Biological Data using Biostrings package in Bioconductor.

Install Packages
Biostrings

Answers to the exercises are available here.

If you obtained a different (correct) answer than those listed on the solutions page, please feel free to post your answer as a comment on that page.

Exercise 1

Create a DNA String and find out the complement of the DNA

Exercise 2

Create a RNA String and find out the complement of the RNA

Exercise 3

Create a DNA string and find the reverse complement of the same.

Exercise 4

Create a RNA string and find the reverse complement of the same.

Exercise 5

Create a DNA string and translate the same into Amino Acids using Standard Genetic codon and print the three letter codon of the amino acids

Exercise 6

Create a DNA string and translate the same into Amino Acids using Standard Genetic codon and print the three letter codon of the amino acids

Exercise 7

Create two DNA Strings and align the sequence using Global Alignment technique and print the score of the alignment

Exercise 8

Create two DNA Strings and align the sequence using Global Alignment technique and print the score of the alignment after specifying your own score for match and mismatch among the sequence

Exercise 9

Create two DNA Strings and align the sequence using Local Alignment technique and print the score of the alignment

Exercise 10

Create two DNA Strings and align the sequence using Overlap Alignment technique and print the score of the alignment

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