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(This article was first published on <strong><a href="http://www.r-exercises.com/2017/06/06/manipulate-biological-data-using-biostrings-package-exercisespart-3/?utm_source=rss&utm_medium=rss&utm_campaign=manipulate-biological-data-using-biostrings-package-exercisespart-3"> R-exercises</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
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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 &amp; Proteins. DNA &amp; 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<br>
In this exercise we try compare between DNAs, RNAs &amp; Amino Acid Sequences to fund out the relationships.<br>
Comparison is done using sequence alignment or sequence comparison techniques.<br>
There are two types of sequence alignment exists.<br>
1.Pairwise alignment<br>
2.Multiple Sequence Alignment</p>
<p>Pairwise alignment refers to comparison between two sequences, where as Multiple Sequence Alignment refers to comparing more than two sequences.</p>
<p>In the exercises below we cover how we can do pairwise alignment using Biostrings package in Bioconductor.</p>
<p>Install Packages<br>
Biostrings</p>
<p>Answers to the exercises are available <a rel="nofollow" href="http://r-exercises.com/2017/06/06/manipulate-biological-data-using-biostrings-package-solutionspart-3/" target="_blank">here</a>.</p>
<p>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.</p>
<p><strong>Exercise 1</strong></p>
<p>Create two DNA strings and do pairwise alignment using local, global and overlap alignment techniques and print the score.</p>
<p><strong>Exercise 2</strong></p>
<p>Create two DNA strings and do pairwise alignment and write the alignment to an .aln file.</p>
<p><strong>Exercise 3</strong></p>
<p>Create two Amino acid strings and do pairwise alignment </p>
<p><strong>Exercise 4</strong></p>
<p>Create two Amino acid strings and do pairwise alignment using BLOSUM62 substitution matrix.</p>
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<div><strong>Learn more</strong> about Data Pre-Processing in the online course <a rel="nofollow" href="http://www.r-exercises.com/product/r-data-pre-processing-data-management-shape-your-data/" target="_blank">R Data Pre-Processing &amp; Data Management – Shape your Data!</a>. In this course you will learn how to:
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<li>use SQL code within R</li>
<li>And much more</li>
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<p><strong>Exercise 5</strong> </p>
<p>Create two Amino acid strings and do pairwise alignment using BLOSUM100 substitution matrix</p>
<p><strong>Exercise 6</strong></p>
<p>Create two Amino acid strings and do pairwise alignment using PAM250 substitution matrix</p>
<p><strong>Exercise 7</strong></p>
<p>Compare between BLOSUM62 substitution matrix of R and that of the NCBI Database using any two amino acid of your choice.</p>
<p><strong>Exercise 8</strong></p>
<p>Do pairwise alignment using Needlemann Wunch Alignment algorithm and print the score, suppress any warnings.</p>
<p><strong>Exercise 9</strong></p>
<p>Create two DNA Strings and translate the same to amino acids and do pairwise alignment between the amino acid sequences</p>
<p><strong>Exercise 10</strong></p>
<p>Create two RNA Strings and translate the same to amino acids and do pairwise alignment between the amino acid sequences</p>
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<h3>Related exercise sets:</h3>
<ol>
<li><a rel="nofollow" href="http://www.r-exercises.com/2017/05/28/manipulate-biological-data-using-biostrings-package-exercises-part-2/" title="Manipulate Biological Data Using Biostrings Package Exercises(Part 2)" target="_blank">Manipulate Biological Data Using Biostrings Package Exercises(Part 2) </a></li>
<li><a rel="nofollow" href="http://www.r-exercises.com/2017/01/22/bioinformatics-lessons-in-r-1-biostrings-exercises/" title="Bioinformatics Tutorial with Exercises in R (part 1)" target="_blank">Bioinformatics Tutorial with Exercises in R (part 1) </a></li>
<li><a rel="nofollow" href="http://www.r-exercises.com/2017/05/10/accessing-and-manipulating-biological-databases-exercises-part-3/" title="Accessing and Manipulating Biological Databases  Exercises (Part-3)" target="_blank">Accessing and Manipulating Biological Databases Exercises (Part-3) </a></li>
<li><a rel="nofollow" href="http://www.r-exercises.com/start-here-to-learn-r/" target="_blank">Explore all our (>1000) R exercises</a></li>
<li><a rel="nofollow" href="http://www.r-exercises.com/r-courses/" target="_blank">Find an R course using our R Course Finder</a> directory</li>
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