Aminoacids

In the past chapters, we have gone through some fundamental ways to analyze and manipulate nucleotide sequences. Now, we'll take a brief look at aminoacid sequences. Luckily, some of the concepts we have implemented for nucleotides also appliy to aminoacids, with some minor tweaking of the code. Examples are:

• Counting aminoacids.
• Identifying homopolymers.
• Hamming distance.
• Global and local aligner (with suitable substitution matrix).

Codon Table

For aminoacids, we have to think triplets of nucleotides because this is what encodes aminoacids. In Rust, we can use something like the bio_seq crate. However, for fun we'll create our own very basic HashMap using the standard NCBI codon table.

use std::collections::HashMap;

fn generate_codon_table<'a>() -> HashMap<[u8; 3], u8> {
    let aa = b"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";

    let base1 = b"TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG";
    let base2 = b"TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG";
    let base3 = b"TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG";

    let map: HashMap<[u8; 3], u8> = (0..aa.len())
        .map(|i| {
            let value = aa[i];
            let key = [base1[i], base2[i], base3[i]];

            return (key, value);
        })
        .collect();

    return map;
}

fn main() {
    let codon_table = generate_codon_table();

    assert_eq!(codon_table.get(b"ATG"), Some(&b'M'));
}