Simple and unoptimized implementations of bioinformatic algorithms in Erlang
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Assembly
- String composition
- Overlapping graph
- DeBruijn graph
- Eulerian path
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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
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Pattern matching
- Trie structure
- Trie match
- Burrows-Wheeler algorithm
- Matching using Burrows-Wheeler
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Sequence rearrangements
- Greeding sorting by reversals
- Number of breakpoints
- 2-break distance
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Sequencing
- Translation
- Amino acid naming functions
- Peptide naming functions
- Peptide encoding
- Mass calc
- Cyclopeptide sequencing
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Suffix Trees
- Suffix Tree
- Suffix Array