Rosalind

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