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 …
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Showing 1–19 of 19 problems
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 …
Protein Molecular Weight
Given a protein string, compute its monoisotopic molecular weight in daltons. Sum the monoisotopic residue mass of each amino acid, …
Sequence Statistics with Comprehensions
You are given a set of DNA sequences. Compute and print, each on its own line: Count: <number of sequences> …
Validating Sequence Records
You are given records, one per line, each supposed to contain an identifier and a DNA sequence separated by a …
Filter Rows by Numeric Threshold
Tab-separated data arrives on standard input. The first line of input is a numeric threshold. The second line is a …
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 …
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 …
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 …
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