Enumerating Gene Orders

Rearrangements Power Large-Scale Genomic Changes

Point mutations can create changes in populations of organisms from the same species, but they lack the power to create and differentiate entire species. This more arduous work is left to larger mutations called genome rearrangements, which move around huge blocks of DNA. Rearrangements cause major genomic change, and most rearrangements are fatal or seriously damaging to the mutated cell and its descendants (many cancers derive from rearrangements). For this reason, rearrangements that come to influence the genome of an entire species are very rare.
Because rearrangements that affect species evolution occur infrequently, two closely related species will have very similar genomes. Thus, to simplify comparison of two such genomes, researchers first identify similar intervals of DNA from the species, called synteny blocks; over time, rearrangements have created these synteny blocks and heaved them around across the two genomes (often separating blocks onto different chromosomes).
A pair of synteny blocks from two different species are not strictly identical (they are separated by the action of point mutations or very small rearrangements), but for the sake of studying large-scale rearrangements, we consider them to be equivalent. As a result, we can label each synteny block with a positive integer; when comparing two species’ genomes/chromosomes, we then only need to specify the order of its numbered synteny blocks.


A permutation of length n is an ordering of the positive integers {1, 2, …, n}. For example, π = (5, 3, 2, 1, 4) is a permutation of length 5.


A positive integer n ≤ 7.


The total number of permutations of length n, followed by a list of all such permutations (in any order).


Let’s import the required package for permutation calculation:

import itertools

Then, we read the dataset:

with open("rosalind_perm.txt") as file:
    N = int(file.read())

We need to define the loop for the permutations. However, in order to print the output as rosalind platform requires, I used a trick here:

def total_permutation(n):
    perm = itertools.permutations(list(range(1, n + 1)))

def permutation(n):
    perm = itertools.permutations(list(range(1, n + 1)))
    for i, j in enumerate(list(perm)):
        permutation_list = ''
        for item in j:
            permutation_list += str(item) + ' '

The functions above return the total number of permutations of length n and list of permutations, respectively. All we need to do is call these function in order:

def enumerating_gene_orders(n):

Finally, we call the main function and return the desired output.

Important note:

This problem is taken from rosalind.info. Please visit ROSALIND to find out more about Bioinformatics problems. You may also clink onto links for the definitions of each terminology.