Longest Shared Motif
Given a collection of DNA strings, find the longest substring that appears in every one of them. The first line …
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Computational Biology
Algorithms and models: dynamic-programming alignment, phylogenetics and hidden Markov models.
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Showing 1–11 of 11 problems
Consensus and Profile Matrix
Given a collection of DNA strings of equal length, build the profile matrix and the consensus string. The first line …
Approximate Motif Matching
Given a DNA string s, a motif t, and a non-negative integer d, find every position where t occurs in …
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 …
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: …
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 …
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