In-silico genome digestion

[ezorita]

Create a C code that digests any genome (from FASTA input) in a reasonable time.

Features:

• Multiple digestion: the code must accept multiple restriction enzymes in the same digestion.
• End annotation: for each generated fragment, annotate the type of cut end, i.e. blunt, AA 3', GATC 5', etc.
• Parser friendly: the output must be easy to parse in C, R (Genomic Ranges), python, etc.

[ezorita]

Update:

• Compact format: Store digestion results in an uncompressed compact data structure.
• Modular digestions: Generate one digestion file per restriction enzyme. Other applications will then combine the digestions to simulate multiple-digestion experiments.
• RE Metadata: Store metadada of the in-silico digestion (Reference genome, RE name, RE sequence, cut en, i.e. 3' and 5' offset from first (5') nucleotide).
• Database-like: Store all digestion files in the same folder, reference files by restriction enzyme name.