Computing GC Content
Given a DNA string, compute the percentage of its bases that are G or C. Print the percentage rounded to …
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Bioinformatics
Applied sequence analysis: motifs, restriction sites, translation, k-mers and assembly.
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Showing 1–19 of 19 problems
Finding a Motif in DNA
Given two DNA strings s and t, find every location where t occurs as a substring of s. Occurrences may …
Restriction Site Palindrome Checker
A DNA string is a reverse-complement palindrome if it is equal to its own reverse complement. Given a DNA string, …
Translating RNA into Protein
Given an RNA string whose length is a multiple of 3, translate it into a protein string using the standard …
Most Frequent k-mers
Given a DNA string text and an integer k, find every k-mer (substring of length k) that occurs the maximum …
RNA Splicing
You are given a DNA string followed by a collection of introns. Remove every occurrence of each intron from the …
Overlap Graphs
Given a collection of DNA strings, build the overlap graph for k = 3: draw a directed edge from string …
Protein Molecular Weight
Given a protein string, compute its monoisotopic molecular weight in daltons. Sum the monoisotopic residue mass of each amino acid, …
Genome Assembly via de Bruijn Graphs
Given a collection of k-mers all of the same length k, build the de Bruijn graph. Each k-mer becomes an …
Sequence Sanitiser
You are given a raw DNA sequence that may contain lowercase letters, ambiguity codes, and N characters. Clean it by …
Primer Melting Temperature
Given a primer sequence, compute its melting temperature (Tm) in degrees Celsius using the Wallace rule for short primers and …
Multi-FASTA Parser
You are given a multi-FASTA file on standard input. Each record begins with a header line starting with >, followed …
k-mer Frequency Array
Given a DNA sequence and an integer k, produce the frequency array: the count of every possible k-mer over the …
Minimum GC Skew
Define Skew(i) as the number of G minus the number of C in the first i characters of a genome, …
Six-Frame ORF Finder
Given a DNA sequence, find every distinct protein string that can be translated from an open reading frame in any …
FASTQ Quality Control
You are given FASTQ records and a quality threshold. Each record is exactly four lines: a header starting with @, …
Locating Restriction Sites
A reverse palindrome is a DNA substring that equals its own reverse complement. Given a DNA sequence, find every reverse …
Transition and Transversion Ratio
You are given two DNA sequences of equal length. At each position where they differ, classify the substitution as either …
Pairwise p-Distance Matrix
You are given several DNA sequences of equal length in multi-FASTA format. For every ordered pair of sequences, compute the …
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