```rust use bio_seq::*;

let seq = dna!("ACTGCTAGCA");

for kmer in seq.kmers::<8>() { println!("{}", kmer); } ```

• bio_seq::alphabet::Dna: DNA use the lexicographically ordered 2-bit representation

• bio_seq::alphabet::Iupac: IUPAC nucleotide ambiguity codes are represented with 4 bits

  ``` A C G T

  ---

  S 0 1 1 0

  • 0 0 0 0 C 0 1 0 0 N 1 1 1 1 B 0 1 1 1 ... etc. ``` This supports membership resolution with bitwise operations:

  rust assert_eq!( format!("{}", iupac!("AS-GYTNA") | iupac!("ANTGCAT-")), "ANTGYWNA" ); assert_eq!( format!("{}", iupac!("ACGTSWKM") & iupac!("WKMSTNNA")), "A----WKA" );

• TODO bio_seq::alphabet::amino: Amino acid sequences

Kmers

Kmers are sequences of DNA with a fixed size. These are implemented with const generics.

Minimisers for free

The 2-bit representation of DNA sequences is lexicographically ordered:

rust // find the lexicographically minimum 8-mer fn minimise(seq: Seq<Dna>) -> Option<Kmer::<8>> { seq.kmers::<8>().min() }

Drop-in compatibility with rust-bio

meant to replace Text/TextSlice

TODO

• benchmarking
• clever bit twiddling hacks for stuff like converting from u8 to 2-bit representation