Count Unique Values in a Stream
A list of values arrives on standard input, one per line. Count how many times each distinct value appears, and …
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Showing 31–52 of 52 problems
Transcribe DNA to RNA with tr
A single DNA sequence arrives on standard input. Transcribe it into RNA by replacing every occurrence of T with U, …
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 …
Mendelian Inheritance Probability
A population contains k homozygous dominant individuals (AA), m heterozygous individuals (Aa), and n homozygous recessive individuals (aa). Two individuals …
Edit Distance
Given two protein or DNA strings, compute their edit distance: the minimum number of insertions, deletions and substitutions required to …
Merge Overlapping Exon Intervals
You are given a set of exon intervals as half-open ranges [start, end) on a single chromosome. Merge every group …
Hardy-Weinberg Equilibrium Test
You are given the observed counts of three genotypes at a biallelic locus: homozygous for the major allele (AA), heterozygous …
CPM Normalisation of a Count Matrix
You are given a gene expression count matrix. The first line is a header with the gene column label followed …
Greedy Motif Search
Given a collection of DNA strings and integers k and t, find a k-mer motif in each of the t …
Median String Motif Finder
Given a set of DNA strings and an integer k, find a median string: the k-mer that minimises the sum, …
Longest Common Subsequence
Given two DNA strings, find a longest common subsequence: the longest string that appears in both as a subsequence, meaning …
UPGMA Phylogenetic Tree
You are given a symmetric distance matrix over n taxa labelled 0 to n-1. Build a UPGMA tree by repeatedly …
Expected Offspring Phenotypes
You are given six integers giving the number of couples in a population with each of these genotype pairings, in …
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