Computational Biology

Algorithms and models: dynamic-programming alignment, phylogenetics and hidden Markov models.

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Status Problem Title Difficulty Tags Action
Longest Shared Motif Advanced Longest Common Substring Motif Dynamic Programming Solve
Consensus and Profile Matrix Advanced Consensus Profile Matrix Alignment Solve
Approximate Motif Matching Advanced Motif Mismatches Approximate Matching Solve
Global Alignment Score with Affine Gap Penalty Advanced Global Alignment Affine Gap Dynamic Programming Solve
Local Alignment Score (Smith-Waterman) Advanced Local Alignment Smith-Waterman Dynamic Programming Solve
Neighbor Joining: First Pair to Merge Advanced Phylogenetics Neighbor Joining Distance Matrix Solve
CpG Island Detection with a Hidden Markov Model Advanced HMM Viterbi CpG Island Solve
Mendelian Inheritance Probability Foundational Probability Mendelian Genetics Combinatorics Formatting Solve
Edit Distance Intermediate Dynamic Programming Alignment Levenshtein Matrices Solve
Merge Overlapping Exon Intervals Intermediate Intervals Sorting Genomic Coordinates Annotation Solve
Hardy-Weinberg Equilibrium Test Intermediate Population Genetics Chi-Square Statistics Allele Frequency Solve
CPM Normalisation of a Count Matrix Intermediate RNA-seq Normalisation Tabular Data Gene Expression Solve
Greedy Motif Search Advanced Motif Finding Greedy Algorithms Profile Matrices Regulatory DNA Solve
Median String Motif Finder Advanced Motif Finding Exhaustive Search Hamming Distance Optimisation Solve
Longest Common Subsequence Advanced Dynamic Programming Traceback Sequence Comparison Alignment Solve
UPGMA Phylogenetic Tree Advanced Phylogenetics Hierarchical Clustering Distance Matrix Newick Solve
Expected Offspring Phenotypes Foundational Probability Expected Value Mendelian Genetics Linearity Solve
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