Function parasailors::local_alignment_score
[−]
[src]
pub fn local_alignment_score(
query_profile: &Profile,
database_sequence: &[u8],
open_cost: i32,
gap_extend_cost: i32
) -> i32
Returns a score for local pairwise alignment using a vectorized version of Smith-Waterman.
Examples
let query = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN"; let profile_ident = Profile::new(query, &identity_matrix); let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTNNNNNNNNN"; assert_eq!(50, local_alignment_score(&profile_ident, reference, 1, 1)); let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTTCCTTTTTTNNNNNNNNN"; assert_eq!(48, local_alignment_score(&profile_ident, reference, 1, 1)); let reference = b"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTTT"; assert_eq!(35, local_alignment_score(&profile_ident, reference, 1, 1));