Repository is for bioinformatics problems from http://www.rosalind.info and the textbook, "Bioinformatics Algorithms - An Active Learning Approach" by Phillip Compeau & Pavel Pevzner.
Completed "Bioinformatics Stronghold" Problems:
| ID | Title |
|---|---|
| DNA | Counting DNA Nucleotides |
| RNA | Transcribing DNA into RNA |
| REVC | Complementing a Strand of DNA |
| FIB | Rabbits and Recurrence Relations |
| GC | Computing GC Content |
| HAMM | Counting Point Mutations |
| IPRB | Mendel's First Law |
| PROT | Translating RNA into Protein |
| SUBS | Finding a Motif in DNA |
| CONS | Consensus and Profile |
| FIBD | Mortal Fibonacci Rabbits |
| GRPH | Overlap Graphs |
| IEV | Calculating Expected Offspring |
| LCSM | Finding a Shared Motif |
| LIA | Independent Alleles |
| MPRT | Finding a Protein Motif |
| MRNA | Inferring mRNA from Protein |
| ORF | Open Reading Frames |
| PERM | Enumerating Gene Orders |
| PRTM | Calculating Protein Mass |
| REVP | Locating Restriction Sites |
| SPLC | RNA Splicing |
| LEXF | Enumerating k-mers Lexicographically |
| LGIS | Longest Increasing Subsequence |
| LONG | Genome Assembly as Shortest Superstring |
| PMCH | Perfect Matchings and RNA Secondary Structures |
| PPER | Partial Permutations |
| PROB | Introduction to Random Strings |
| SIGN | Enumerating Oriented Gene Orderings |
| SSEQ | Finding a Spliced Motif |
| TRAN | Transitions and Transversions |
| TREE | Completing a Tree |
| CAT | Catalan Numbers and RNA Secondary Structures |
| CORR | Error Correction in Reads |
| INOD | Counting Phylogenetic Ancestors |
| KMER | k-Mer Composition |
| KMP | Speeding Up Motif Finding |
| LCSQ | Finding a Shared Spliced Motif |
| LEXV | Ordering Strings of Varying Length Lexicographically |
| MMCH | Maximum Matchings and RNA Secondary Structures |
| PDST | Creating a Distance Matrix |
| REAR | Reversal Distance |
| RSTR | Matching Random Motifs |
| SSET | Counting Subsets |
| ASPC | Introduction to Alternative Splicing |
| EDIT | Edit Distance |
| EVAL | Expected Number of Restriction Sites |
| MOTZ | Motzkin Numbers and RNA Secondary Structures |
| NWCK | Distances in Trees |
| SCSP | Interleaving Two Motifs |
| SETO | Introduction to Set Operations |
| SORT | Sorting by Reversals |
| SPEC | Inferring Protein from Spectrum |
| TRIE | Introduction to Pattern Matching |
| CONV | Comparing Spectra with the Spectral Convolution |
| CTBL | Creating a Character Table |
| DBRU | Constructing a De Bruijn Graph |
| EDTA | Edit Distance Alignment |
| FULL | Inferring Peptide from Full Spectrum |
| INDC | Independent Segregation of Chromosomes |
| ITWV | Finding Disjoint Motifs in a Gene |
| LREP | Finding the Longest Multiple Repeat |
| NKEW | Newick Format with Edge Weights |
| RNAS | Wobble Bonding and RNA Secondary Structures |
| AFRQ | Counting Disease Carriers |
| CTEA | Counting Optimal Alignments |
| GLOB | Global Alignment with Scoring Matrix |
| SGRA | Using the Spectrum Graph to Infer Peptides |
| GCON | Global Alignment with Constant Gap Penalty |
| LOCA | Local Alignment with Scoring Matrix |
| MGAP | Maximizing the Gap Symbols of an Optimal Alignment |
| MULT | Multiple Alignment |
| SEXL | Sex-Linked Inheritance |
| GAFF | Global Alignment with Scoring Matrix and Affine Gap Penalty |
| OAP | Overlap Alignment |
| SIMS | Finding a Motif with Modifications |
| SMGB | Semiglobal Alignment |
| LAFF | Local Alignment with Affine Gap Penalty |
| OSYM | Isolating Symbols in Alignments |
| MEND | Inferring Genotype from a Pedigree |
| CSTR | Creating a Character Table from Genetic Strings |
| WFMD | The Wright-Fisher Model of Genetic Drift |
| EBIN | Wright-Fisher's Expected Behavior |
| FOUN | The Founder Effect and Genetic Drift |
| CUNR | Counting Unrooted Binary Trees |
| ROOT | Counting Rooted Binary Trees |
| PCOV | Genome Assembly with Perfect Coverage |
| ASMQ | Assessing Assembly Quality with N50 and N75 |
| GASM | Genome Assembly Using Reads |
Unfinished "Bioinformatics Stronghold" Problems:
| ID | Title |
|---|---|
| PRSM | Matching a Spectrum to a Protein |
| QRT | Quartets |
| SUFF | Encoding Suffix Trees |
| KSIM | Finding All Similar Motifs |
| CHBP | Character-Based Phylogeny |
| CNTQ | Counting Quartets |
| EUBT | Enumerating Unrooted Binary Trees |
| LING | Linguistic Complexity of a Genome |
| MREP | Identifying Maximal Repeats |
| PDPL | Creating a Restriction Map |
| SPTD | Phylogeny Comparison with Split Distance |
| ALPH | Alignment-Based Phylogeny |
| CSET | Fixing an Inconsistent Character Set |
| GREP | Genome Assembly with Perfect Coverage and Repeats |
| QRTD | Quartet Distance |
| RSUB | Identifying Reversing Substitutions |