Calculate the Hamming difference between two DNA strands.
A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.
The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.
By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.
This is called the 'Hamming distance'.
It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.
GAGCCTACTAACGGGAT CATCGTAATGACGGCCT ^ ^ ^ ^ ^ ^^
The Hamming distance between these two DNA strands is 7.
The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.
For installation and learning resources, refer to the exercism help page.
To work on the exercises, you will need
Base. Consult opam website for instructions on how to install
opam for your OS. Once
opam is installed open a terminal window and run the following command to install base:
opam install base
To run the tests you will need
OUnit. Install it using
opam install ounit
A Makefile is provided with a default target to compile your solution and run the tests. At the command line, type:
utop is a command line program which allows you to run Ocaml code interactively. The easiest way to install it is via opam:
opam install utop
Consult utop for more detail.
The exercism/ocaml repository on GitHub is the home for all of the Ocaml exercises.
If you have feedback about an exercise, or want to help implementing a new one, head over there and create an issue. We'll do our best to help you!
The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/
It's possible to submit an incomplete solution so you can see how others have completed the exercise.
open Base open OUnit2 open Hamming let printer = function | None -> "None" | Some x -> Int.to_string x let ae exp got _test_ctxt = assert_equal ~printer exp got let dna_of_string s = let f = function | 'A' -> A | 'C' -> C | 'G' -> G | 'T' -> T | _ -> failwith "Big news! New nucleotide discovered" in String.to_list s |> List.map ~f let hamdist a b = hamming_distance (dna_of_string a) (dna_of_string b) let tests = [ "empty strands" >:: ae (Some 0) (hamdist "" ""); "identical strands" >:: ae (Some 0) (hamdist "A" "A"); "long identical strands" >:: ae (Some 0) (hamdist "GGACTGA" "GGACTGA"); "complete distance in single nucleotide strands" >:: ae (Some 1) (hamdist "A" "G"); "complete distance in small strands" >:: ae (Some 2) (hamdist "AG" "CT"); "small distance in small strands" >:: ae (Some 1) (hamdist "AT" "CT"); "small distance" >:: ae (Some 1) (hamdist "GGACG" "GGTCG"); "small distance in long strands" >:: ae (Some 2) (hamdist "ACCAGGG" "ACTATGG"); "non-unique character in first strand" >:: ae (Some 1) (hamdist "AAG" "AAA"); "non-unique character in second strand" >:: ae (Some 1) (hamdist "AAA" "AAG"); "same nucleotides in different positions" >:: ae (Some 2) (hamdist "TAG" "GAT"); "large distance" >:: ae (Some 4) (hamdist "GATACA" "GCATAA"); "large distance in off-by-one strand" >:: ae (Some 9) (hamdist "GGACGGATTCTG" "AGGACGGATTCT"); "disallow first strand longer" >:: ae None (hamdist "AATG" "AAA"); "disallow second strand longer" >:: ae None (hamdist "ATA" "AGTG"); ] let () = run_test_tt_main ("hamming tests" >::: tests)
type nucleotide = A | C | G | T let hamming_distance (l1 : nucleotide list) (l2 : nucleotide list) = try Some ( List.fold_left2 (fun a e1 e2 -> if e1 = e2 then a else a + 1) 0 l1 l2) with Invalid_argument _ -> None
A huge amount can be learned from reading other people’s code. This is why we wanted to give exercism users the option of making their solutions public.
Here are some questions to help you reflect on this solution and learn the most from it.