Skip to main content

Questions tagged [bioinformatics]

Bioinformatics is the use of software tools to analyse biological data.

Filter by
Sorted by
Tagged with
6 votes
3 answers
1k views

The Genetic Code

This question is part of a series solving the Rosalind challenges. For the previous question in this series, see Wascally wabbits. The repository with all my up-to-date solutions so far can be found ...
Mast's user avatar
  • 13.4k
19 votes
2 answers
597 views

Count the occurence of nucleobases in DNA string

Inspired by this meta question I decided to take a look at Rosalind. Their first challenge seemed easy enough: An example of a length 21 DNA string (whose alphabet contains the symbols 'A', 'C', 'G', ...
Mast's user avatar
  • 13.4k
4 votes
1 answer
124 views

A small protein database

I am making a small database and these are the following files. The scripts are working. How can I improve my scripts? Are there any places where a problem could occur? I have yet to write tests for ...
catuf's user avatar
  • 433
11 votes
1 answer
135 views

Python genetic sequence visualizer

I'm a beginner at python, and this is my first major project. Inspired by this reddit post, I wrote a program that accepts a DNA sequence (in a FASTA file format) and generates a graphical ...
logwet's user avatar
  • 175
8 votes
1 answer
545 views

Calculating protein mass

This question is part of a series solving the Rosalind challenges. For the previous question in this series, see A sequence of mistakes. The repository with all my up-to-date solutions so far can be ...
Mast's user avatar
  • 13.4k
6 votes
1 answer
473 views

GenBank to FASTA format using regular expressions without Biopython

This is a Biopython alternative with pretty straightforward code. How can I make this more concise? ...
Ethan Hetrick's user avatar
6 votes
2 answers
1k views

Genomic Range Query

Recently I worked on one of the Codility Training - Genomic Range Query (please refer to one of the evaluation report for the detail of this training). The proper approach for this question is using ...
Ming-Chen's user avatar
6 votes
2 answers
261 views

Genetic Sequence Visualizer - Generating large images

Inspired by this reddit post, I have written a program that accepts a DNA sequence (in a FASTA file format) and generates a graphical representation. HIV virus and Ebola virus My program works like ...
logwet's user avatar
  • 175
5 votes
4 answers
917 views

Counting nucleobases in a nucleotide

This question is part of a series solving the Rosalind challenges. For the previous question in this series, see Calculating protein mass ruby. The repository with all my up-to-date solutions so far ...
Mast's user avatar
  • 13.4k
3 votes
1 answer
69 views

Run an external program and extract a pattern match along with the result file

The script takes two input files of protein sequences and runs an external program (installed in linux/MacOS). The result provides a text output file example output.. Identity percentage is extracted ...
catuf's user avatar
  • 433
3 votes
1 answer
89 views

A Java class for reading MaCH dosage files

A dosage file (used in computational genetics) is formatted like this: ...
qed's user avatar
  • 1,419
2 votes
2 answers
118 views

A sequence of mistakes

This question is part of a series solving the Rosalind challenges. For the previous question in this series, see The Genetic Code. The repository with all my up-to-date solutions so far can be found ...
Mast's user avatar
  • 13.4k
2 votes
1 answer
53 views

A Java class for reading MaCH dosage files v2.0

Version 2 of A Java class for reading MaCH dosage files ...
qed's user avatar
  • 1,419