Counting Nucleotides
Given a single-stranded DNA sequence composed only of the characters A, C, G and T, count how many times each …
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DNA to RNA Transcription
Given a DNA string representing the coding strand, produce the corresponding RNA string by replacing every T with U. All …
Reverse Complement
Given a DNA string, return its reverse complement: take the complement of each base (A to T, T to A, …
Computing GC Content
Given a DNA string, compute the percentage of its bases that are G or C. Print the percentage rounded to …
Hamming Distance
Given two DNA strings of equal length, count the positions at which their symbols differ. This is the Hamming distance. …
Sequence Report Card
Read a sequence identifier on the first line and a DNA sequence on the second line. Print a three-line report: …
Filter Sequences by Length
You are given a minimum length and a list of DNA sequences. Print every sequence whose length is greater than …
Codon Usage Counter
Given a coding DNA sequence, split it into non-overlapping codons of three bases, starting at position 0, and count how …
Trim Adapter Sequences
You are given an adapter sequence and a set of reads. For each read, if the adapter appears anywhere in …
Count Sequences in a FASTA Stream
FASTA-formatted text arrives on standard input. Every record begins with a header line whose first character is >. Print a …
Extract FASTA Identifiers
FASTA-formatted text arrives on standard input. For every header line, print the identifier: the header text with the leading > …
Extract a Column from a TSV Stream
Tab-separated text arrives on standard input. The first line is a header and must be skipped. The first line of …
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 …
Mendelian Inheritance Probability
A population contains k homozygous dominant individuals (AA), m heterozygous individuals (Aa), and n homozygous recessive individuals (aa). Two individuals …
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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