Counting Nucleotides
Given a single-stranded DNA sequence composed only of the characters A, C, G and T, count how many times each …
PRACTICE · EXPLORE · IMPROVE
Problem bank
Find your next bioinformatics challenge and work through it at your pace.
Filters
Difficulty
Category
Tags
Showing 1–30 of 52 problems
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. …
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 …
Longest Shared Motif
Given a collection of DNA strings, find the longest substring that appears in every one of them. The first line …
RNA Splicing
You are given a DNA string followed by a collection of introns. Remove every occurrence of each intron from the …
Consensus and Profile Matrix
Given a collection of DNA strings of equal length, build the profile matrix and the consensus string. The first line …
Overlap Graphs
Given a collection of DNA strings, build the overlap graph for k = 3: draw a directed edge from string …
Approximate Motif Matching
Given a DNA string s, a motif t, and a non-negative integer d, find every position where t occurs in …
Protein Molecular Weight
Given a protein string, compute its monoisotopic molecular weight in daltons. Sum the monoisotopic residue mass of each amino acid, …
Global Alignment Score with Affine Gap Penalty
Compute the optimal global alignment score of two DNA strings under an affine gap model. Scoring: match: +1 mismatch: -1 …
Local Alignment Score (Smith-Waterman)
Compute the optimal local alignment score of two DNA strings using the Smith-Waterman algorithm. Scoring: match: +2 mismatch: -1 gap …
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 …
Neighbor Joining: First Pair to Merge
Given a symmetric distance matrix over n taxa, determine which pair neighbor joining merges first. Neighbor joining does not pick …
CpG Island Detection with a Hidden Markov Model
Given a DNA sequence, use Viterbi decoding to find the most likely sequence of hidden states. There are two states: …
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 …
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 …
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 …
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 …
No matches on this page.
There could still be a hit elsewhere in the bank — run a full search to check.
There could still be a hit elsewhere in the bank — run a full search to check.