Rosalind — Bioinformatics Stronghold

Worked solutions to all 105 problems of the Rosalind Bioinformatics Stronghold. See the problem list.

105 problems — 105 solved, 0 partial. 105 carry assertions that run on every commit; 1 need a network connection and are checked separately. Press Run on any block to execute it in your browser, or open the whole pack in the workbench.

Take it with you: download this page as a notebook (.bln — run it with bl notebook, or export it to HTML, PDF or Jupyter), every problem as a zip, or grab a single problem with the Download .bl link in its section.

Sections

Or read every problem on a single page — heavier to load, but one place to scroll, search and print.

Sequence

10 problems — 10 solved

DNA, RNA, REVC, HAMM, GC, TRAN, CONS, REVP, CORR, KMER

Combinatorics

15 problems — 15 solved

FIB, FIBD, MRNA, PERM, PPER, SSET, PMCH, MMCH, CAT, LEXF, SIGN, LEXV, ASPC, MOTZ, PDPL

Translation

2 problems — 2 solved

PROT, SPLC

Motifs

6 problems — 6 solved

SUBS, LCSM, SSEQ, MPRT, ITWV, KSIM

Probability

12 problems — 12 solved

IPRB, IEV, LIA, SEXL, AFRQ, PROB, EVAL, EBIN, INDC, WFMD, RSTR, FOUN

Protein

1 problem — 1 solved

PRTM

Alignment

14 problems — 14 solved

EDIT, GLOB, LOCA, GAFF, OAP, SIMS, EDTA, CTEA, GCON, LAFF, SMGB, MGAP, MULT, OSYM

Graphs

2 problems — 2 solved

GRPH, DBRU

Phylogeny

19 problems — 19 solved

TREE, INOD, PDST, ROOT, CUNR, NWCK, NKEW, CTBL, SPTD, MEND, CSET, CSTR, ALPH, CNTQ, QRT, CHBP, EUBT, QRTD, RSUB

Dynamic programming

3 problems — 3 solved

LGIS, LCSQ, SCSP

Assembly

5 problems — 5 solved

ASMQ, LONG, PCOV, GASM, GREP

Orf

1 problem — 1 solved

ORF

Sets

1 problem — 1 solved

SETO

Strings

6 problems — 6 solved

KMP, TRIE, LING, LREP, MREP, SUFF

Mass spectrometry

5 problems — 5 solved

SPEC, CONV, PRSM, SGRA, FULL

Rna

1 problem — 1 solved

RNAS

Rearrangements

2 problems — 2 solved

REAR, SORT

Every problem

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