91 lines
3.2 KiB
Markdown
91 lines
3.2 KiB
Markdown
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# Hamming
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Write a program that can calculate the Hamming difference between two DNA strands.
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A mutation is simply a mistake that occurs during the creation or
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copying of a nucleic acid, in particular DNA. Because nucleic acids are
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vital to cellular functions, mutations tend to cause a ripple effect
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throughout the cell. Although mutations are technically mistakes, a very
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rare mutation may equip the cell with a beneficial attribute. In fact,
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the macro effects of evolution are attributable by the accumulated
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result of beneficial microscopic mutations over many generations.
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The simplest and most common type of nucleic acid mutation is a point
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mutation, which replaces one base with another at a single nucleotide.
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By counting the number of differences between two homologous DNA strands
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taken from different genomes with a common ancestor, we get a measure of
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the minimum number of point mutations that could have occurred on the
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evolutionary path between the two strands.
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This is called the 'Hamming distance'.
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It is found by comparing two DNA strands and counting how many of the
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nucleotides are different from their equivalent in the other string.
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GAGCCTACTAACGGGAT
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CATCGTAATGACGGCCT
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^ ^ ^ ^ ^ ^^
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The Hamming distance between these two DNA strands is 7.
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# Implementation notes
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The Hamming distance is only defined for sequences of equal length. This means
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that based on the definition, each language could deal with getting sequences
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of equal length differently.
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## Setup
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Check out [Exercism Help](http://exercism.io/languages/lisp) for instructions to
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get started writing Common Lisp. That page will explain how to install and setup
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a Lisp implementation and how to run the tests.
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## Formatting
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While Common Lisp doesn't care about indentation and layout of code,
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nor whether you use spaces or tabs, this is an important consideration
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for submissions to exercism.io. Excercism.io's code widget cannot
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handle mixing of tab and space characters well so using only spaces is recommended to make
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the code more readable to the human reviewers. Please review your
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editors settings on how to accomplish this. Below are instructions for
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popular editors for Common Lisp.
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### VIM
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Use the following commands to ensure VIM uses only spaces for
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indentation:
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```vimscript
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:set tabstop=2
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:set shiftwidth=2
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:set expandtab
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```
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(or as a oneliner `:set tabstop=2 shiftwidth=2 expandtab`). This can
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be added to your `~/.vimrc` file to use it all the time.
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### Emacs
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Emacs is very well suited for editing Common Lisp and has many
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powerful add-on packages available. The only thing that one needs to
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do with a stock emacs to make it work well with exercism.io is to
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evaluate the following code:
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`(setq indent-tab-mode nil)`
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This can be placed in your `~/.emacs` (or `~/.emacs.d/init.el`) in
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order to have it set whenever Emacs is launched.
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One suggested add-on for Emacs and Common Lisp is
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[SLIME](https://github.com/slime/slime) which offers tight integration
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with the REPL; making iterative coding and testing very easy.
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## Source
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The Calculating Point Mutations problem at Rosalind [http://rosalind.info/problems/hamm/](http://rosalind.info/problems/hamm/)
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## Submitting Incomplete Problems
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It's possible to submit an incomplete solution so you can see how others have completed the exercise.
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