Lecture 8 - Finishing alignments

Continuing from Lab07

Alignment tracing for NW and SW

• start from $M_{(i,j)}$ where $i$ and $j$ are

  • the last indices in 1st and 2nd dimension for NW

  • the indices for the matrix with the maximum score in SW

• Check the score from

  1. $M_{(i,j-1)}$ (cell to the left), a gap score

  2. $M_{(i-1,j)}$ (cell above), a gap score

  3. $M_{(i-1,j-1)}$ (cell from diagonal), a match or mismatch

• If any match your current cell, push correct characters to alignments

  1. push gap to seq1, character at $j$ to seq2

  2. push character at $i$ to seq1, gap to seq2

  3. push character at $i$ to seq1, character at $j$ to =seq2=

• update indices

Special considerations

• Be mindful of what happens when you hit the first row or first column

  • $i-1$ or $j-1$ may throw bounds error

• When should your loop stop?

  • It will be different for Needleman-Wunsch than for Smith-Waterman

A test suite:

@testset "Lab07" begin
    @test nwalign("AATTGGCC", "AATTTGCC") == ("AATTGGCC", "AATTTGCC")
    @test any(aln -> aln == nwalign("AATTGGCC", "AAGGTTCC"), [
            ("AA--TTGGCC", "AAGGTT--CC"),
            ("AATTGGCC", "AAGGTTCC")])
    @test nwalign("AATTGGCC", "AAGGTTCC", gap=-2) == ("AATTGGCC", "AAGGTTCC")
    @test nwalign("AATTGGCC", "AAGGTTCC", mismatch=-2) == ("AA--TTGGCC", "AAGGTT--CC")

    @test swalign("AAT", "AA") == ("AA", "AA")
    @test swalign("AAAAATTGGCCAAAAA", "ATTGGCCA") == ("ATTGGCCA", "ATTGGCCA")
    @test swalign("AAAAATTGGCCAAAAA", "ATTGGCAAA") == ("ATTGGCCAAA", "ATTGGC-AAA")
end