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Questions tagged [rosalind]

Rosalind is a platform for learning bioinformatics through problem solving.

56 questions
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With Python, I want to add the last two values of a string but I want to keep double digit numbers together and not include spaces in the string index

I need to create a fibonacci sequence (k = 5, until 5 elements are in the sequence) from an original string containing two starting values. While calling the last two elements in the string forward (newnumber= old[-1] + old[-2]) I pull the number…
Dylan Ellis
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Rosalind - Consensus and Profile - Issue with answer formatting

I am working on the Consensus and Profile problem on Rosalind, and I am so close to getting it done. My answer is correct, I have the right consensus string and the correct matrix, but I am having issues formatting my data for the answer. Rosalind…
danielpintard
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Rosalind Translating RNA into Protein problem

Hello i tried doing this problem from ROSALIND but when i put the example rna sequence (AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA) it produced me the wrong output "['M', 'M', 'N', 'I']" instead of the suggested "MAMAPRTEINSTRING".I tried…
Mike Andrew
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Cumulative Binomial Probability Python

I tried to calculate the Cumulative Binomial Probability to resolve the "Independent Alleles" problem from Rosalind, and I think I got the program right but the result gives me "wrong" every time. The problem: Given: Two positive integers k (k≤7)…
MarianaZ
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I can't use properly the replace command in python

I'm new on the platform: I have a doubt about the use of the replace command. Here is my code and what I need to do: The thing is that I need to replace a substring with a string sequence. For example: from: Hitacoworld to Hiworld. The thing is that…
dananada
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Rosalind Consensus and Profile Problem code doesn't work

This is the problem: http://rosalind.info/problems/cons/ def file_read(fname): with open(fname, "r") as myfile: global data data = myfile.readlines() print(data) i = 0 while i < len(data): …
sickleox2
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How can I improve the speed of my R code regarding shortest substring implementation problem?

I decided to implement this problem from Rosalind in R. It works great for small sample dataset: >Rosalind_56 ATTAGACCTG >Rosalind_57 CCTGCCGGAA >Rosalind_58 AGACCTGCCG >Rosalind_59 GCCGGAATAC however it takes long time when I run it for real…
Adamm
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Want to find the positions where a pattern (substring) starts in another string in python

Input: strA = "ATATATGCGATAT" strB = "ATAT" output: 0 2 9 I was looking for a way to find the starting positions in a string (strA), every time a pattern (strB) starts.
Sukanta
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I couldn't understand the cause of that name error

I am trying to solve the problems at http://rosalind.info/problems/list-view/ and there is a problem called IPRB.In short, we have 3 different organisms k(homozygote dominant), m(heterozygote) and n(homozygote recessive). It asks you to calculate…
Mehmet İzmirli
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How to write a string algorithm

given a FASTA text file (Rosalind_gc.txt), I am supposed to go through each DNA record and identify the percentage (%) of Guanine-Cytosine (GC) content. Example of this is : Sample…
Thomas William Dunn
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Consensus string & profile matrix

I have written the following python code to solve one of the Rosalind problems (http://rosalind.info/problems/cons/) and for some reason, Rosalind says the answer is wrong but I did some spot-checking and it appears right. The problem is as…
Radwa Sharaf
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Mortal Fibonacci Rabbits -error at values greater than 6

I try to count Mortal Fibonacci Rabbits. The task assumes that rabbits die out after a fixed number of months. The picture shows how the number of rabbits changes over time Rabbits The Fibonacci sequence for Mortal Rabbits looks like…
agro
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Rosalind's - 'Ordering Strings of Varying Length Lexicographically' Is it possible to sort my result?

I tried to solve another of Rosalind(http://rosalind.info/problems/lexv/) problems by myself, however unfortunately I have to ask you for help. Here is my approach: First of all; function which creates all possible substrings of input string with…
Adamm
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Rosalind Consensus and Profile

I am trying to solve the question from here http://rosalind.info/problems/cons/ My script fills the counter lists and outputs a consensus string of equal length. I don't think there are math or index errors going on and have run into a wall. My…
Sank Finatra
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Rosalind Profile and Consensus: Writing long strings to one line in Python (Formatting)

I'm trying to tackle a problem on Rosalind where, given a FASTA file of at most 10 sequences at 1kb, I need to give the consensus sequence and profile (how many of each base do all the sequences have in common at each nucleotide). In the context of…
Callen Bragdon
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