Bioinformatics Problem Bank — Practice & Solve

Status	Problem Title	Difficulty	Tags	Action
	Counting Nucleotides	Foundational	DNA Strings Counting	Solve
	DNA to RNA Transcription	Foundational	Transcription DNA RNA	Solve
	Reverse Complement	Foundational	DNA Reverse Complement Double Helix	Solve
	Computing GC Content	Foundational	GC Content DNA Statistics	Solve
	Hamming Distance	Foundational	Hamming Distance Point Mutation Comparison	Solve
	Finding a Motif in DNA	Intermediate	Motif Substring Pattern Matching	Solve
	Restriction Site Palindrome Checker	Intermediate	Restriction Enzyme Palindrome Reverse Complement	Solve
	Translating RNA into Protein	Intermediate	Translation Codon Protein	Solve
	Most Frequent k-mers	Intermediate	k-mer Frequency Motif Discovery	Solve
	Longest Shared Motif	Advanced	Longest Common Substring Motif Dynamic Programming	Solve
	RNA Splicing	Intermediate	Splicing Intron Translation	Solve
	Consensus and Profile Matrix	Advanced	Consensus Profile Matrix Alignment	Solve
	Overlap Graphs	Advanced	Overlap Graph Assembly Graph	Solve
	Approximate Motif Matching	Advanced	Motif Mismatches Approximate Matching	Solve
	Protein Molecular Weight	Intermediate	Protein Mass Spectrometry Molecular Weight	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
	Genome Assembly via de Bruijn Graphs	Advanced	de Bruijn Graph Assembly k-mer	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
	Sequence Report Card	Foundational	Python Variables Basic I/O String Formatting	Solve
	Filter Sequences by Length	Foundational	Python Lists Loops Conditionals	Solve
	Codon Usage Counter	Foundational	Python Dictionaries Chunking Sorting	Solve
	Trim Adapter Sequences	Foundational	Python String Methods Slicing Read Trimming	Solve
	Sequence Statistics with Comprehensions	Intermediate	Python List Comprehensions Aggregation Formatting	Solve
	Validating Sequence Records	Intermediate	Python Error Handling Validation Data Quality	Solve
	Count Sequences in a FASTA Stream	Foundational	Bash grep Counting FASTA	Solve
	Extract FASTA Identifiers	Foundational	Bash grep sed Text Processing	Solve
	Extract a Column from a TSV Stream	Foundational	Bash awk cut Tabular Data	Solve
	Filter Rows by Numeric Threshold	Intermediate	Bash awk Filtering Differential Expression	Solve
	Count Unique Values in a Stream	Intermediate	Bash sort uniq Pipelines Aggregation	Solve
	Transcribe DNA to RNA with tr	Foundational	Bash tr sed Character Substitution	Solve
	Sequence Sanitiser	Foundational	DNA Sets Filtering Data Cleaning	Solve
	Primer Melting Temperature	Foundational	PCR Conditionals Functions Formatting	Solve
	Multi-FASTA Parser	Foundational	FASTA Parsing File Formats Records	Solve
	k-mer Frequency Array	Foundational	k-mers Counting Lexicographic Order Sliding Window	Solve
	Minimum GC Skew	Intermediate	GC Skew Cumulative Sums Replication Origin Genomics	Solve
	Six-Frame ORF Finder	Intermediate	ORF Translation Reading Frames Gene Prediction	Solve
	FASTQ Quality Control	Intermediate	FASTQ Phred Scores Quality Control Parsing	Solve
	Locating Restriction Sites	Intermediate	Restriction Enzymes Palindromes Nested Loops Cloning	Solve
	Transition and Transversion Ratio	Intermediate	Mutations Molecular Evolution Ratios Formatting	Solve
	Pairwise p-Distance Matrix	Advanced	Distance Matrix Phylogenetics FASTA Formatting	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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