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Developing Hash Functions and Sequence Alignment Scripts in Perl

This assignment focuses on using hashes to manage and analyze genome data effectively. First, create a script that prints a hash sorted by keys in alphabetical order and implement a method to remove an entry from the hash. Next, write a program that calculates mono-, di-, tri-, and quartet-nucleotide frequencies in a genome using hashes. Additionally, turn your project outline into a detailed to-do list or pseudocode. Finally, develop a Perl script that utilizes MUSCLE or ClustalW2 to align multiple non-aligned sequence files in a specified directory and compute profile alignments among the aligned sequences.

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Developing Hash Functions and Sequence Alignment Scripts in Perl

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  1. Assignments # 9 (due 3/13): Write a script that prints out a hash sorted on the keys in alphabetical order. How can you remove an entry in a hash (key and value)? Write a program that it uses hashes to calculates mono-, di-, tri-, and quartet-nucleotide frequencies in a genome. Turn your project outline into a step by step to-do list / pseudocode

  2. assignments continued • Assume that you have the following non-aligned multiple sequence files in a directory: A.fa : vacuolar/archaeal ATPase catalytic subunits ; B.fa : vacuolar/archaeal ATPase non-catalytic subunits;alpha.fa : F-ATPases non-catalytic subunits,beta.fa : F-ATPases catalytic subunits,F.fa : ATPase involved in the assembly of the bacterial flagella. • Write a perl script that executes muscle or clustalw2 and • aligns the sequences within each file • successively calculates profile alignments between all aligned sequences.

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