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https://github.com/mattdoug604/rosalind

A repository for my solutions to problems from - http://www.rosalind.info
https://github.com/mattdoug604/rosalind

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A repository for my solutions to problems from - http://www.rosalind.info

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README 

        
# 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