Questions tagged [rosalind]
Rosalind is a platform for learning bioinformatics through problem solving.
rosalind
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Problem with Object Types operations in Julia for solving Rosalind problem "Open Reading Frames"
Code context: I am trying to solve the Rosalind problem "Open Reading Frames" (https://rosalind.info/problems/orf/). The approach I am using involves storing each ORF result in a variable ...
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1
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99
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Finding longest common substring between DNA sequences (Python)
I am working on the "Finding a shared motif" problem from rosalind.info (https://rosalind.info/problems/lcsm/). This problem asks you to find the longest common substring in a collection of &...
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Solving the Rosalind challenge "Finding a Motif in DNA" [duplicate]
The problem I am currently working on gives you a DNA string and a substring. You need to have your code output the start location of each instance of the substring in the DNA string. For ex;
given ...
- 33
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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 (...
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1
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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 ...
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1
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209
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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']&...
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204
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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&...
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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:...
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1
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478
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Python - Rosalind Open Reading Frame Problem
There's an Open Reading Frame exercise on Rosalind, for which I get different results from what is obtained in the example task. The exercise description can be found here.
I have this code:
gencode = ...
-1
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2
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195
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Python Regex Finding a Match That Starts Inside Previous match [duplicate]
I'm looking to find the index for all substrings in a string in python. My current regex code can't find a match that has it's start in a previous match.
I have a string: s = r'GATATATGCATATACTT' and ...
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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)
...
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answers
93
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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
...
- 2,306
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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.
- 75
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Python: Rosalind Consensus and Profile
I am trying to solve the "Consensus and Profile" challenge on Rosalind.
The challenge instructions are as follows:
Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in ...
- 153
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Count frequency of values in pandas DataFrame
Having this pandas.core.frame.DataFrame:
Gorilla A T C C A G C T
Dog G G G C A A C T
Humano A T G G A T C T
Drosophila A A G C A A C C
Elefante T T ...
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