All Questions
Tagged with bioinformaticsc++
9 questions
5votes
3answers
1kviews
DNA reverse complement as fast as possible
This code is meant to compute the reverse complement for a given sequence of bases. The code is tested versus some test cases and seems to work so far. The primary goal is that it should be as fast ...
- 153
2votes
1answer
242views
Push Down Automaton to detect RNA hairpins
For one of my assignments I am supposed to write a Push Down Automaton. It's supposed to receive a string that has to be checked if it's an RNA Hairpin. For example: gacgcaaguc would be one, since ...
10votes
3answers
2kviews
A simple C++ class for packing DNA strings
Introduction I have this small C++ program that packs a DNA string over alphabet ACGT into a bit vector, two bits per character. Code dnapack.hpp ...
- 30.2k
9votes
3answers
960views
Simple program to split DNA sequences based on ambiguous content
The problem I have a program that takes a file of DNA sequences as input and writes each entry to one of two output files: one file for sequences containing only canonical characters (...
- 1,069
5votes
1answer
818views
Reading string from a text file and returning the number of occurrences of each substring of length k
This program takes a simple nucleotide sequence and finds the most common "k-mers" in the sequence, as determined by the supplied dataset (see below). The goal of the program is to find the origin of ...
2votes
0answers
71views
Determining if a genetic sequence is palindromic
Adding another level to my previous question on 'normal' palindrome identification, in this one I'm interested in identifying genetic palindromes. Here's my attempt: ...
- 825
4votes
2answers
1kviews
DNA base pair match counter
So my code is done it outputs exactly what it needs to I'm just wondering if it is possible to make this code a lot more simple using objects. If so could someone tell me what I would need member-wise ...
5votes
1answer
687views
SAM mapped reads
I write quite a bit of code in C, but haven't done much C++ since my college CS classes. I have been revisiting C++ recently, and thought I would re-implement a program I had previously written in C, ...
- 1,069
8votes
3answers
576views
Statistical calculations with sets of genes
The following piece of code executes 20 million times each time the program is called, so I need a way to make this code as optimized as possible. ...
- 191
