karlll / bioerl

Bioinformatics in Erlang

bioerl

Bioinformatic algorithms in Erlang

Simple and unoptimized implementations of bioinformatic algorithms in Erlang

• Assembly

  • String composition
  • Overlapping graph
  • DeBruijn graph
  • Eulerian path

• Comparing sequences

  • Longest common subsequence
  • Longest path in DAG
  • Global alignment graph
  • Local Alignment
  • Levenshtein Distance
  • Fitting Alignment
  • Overlappign align

• Finding

  • Motif enum
  • Mean string
  • Profile most probable k-mer
  • Frequency
  • Complement
  • Find substrings
  • Find clumps
  • Skew
  • Approx. pattern matching

• Pattern matching

  • Trie structure
  • Trie match
  • Burrows-Wheeler algorithm
  • Matching using Burrows-Wheeler

• Sequence rearrangements

  • Greeding sorting by reversals
  • Number of breakpoints
  • 2-break distance

• Sequencing

  • Translation
  • Amino acid naming functions
  • Peptide naming functions
  • Peptide encoding
  • Mass calc
  • Cyclopeptide sequencing

• Suffix Trees

  • Suffix Tree
  • Suffix Array