ls11-www.cs.tu-dortmund.de/_media/staff/kopczyns/meds-for-bs.pdf
A 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 3, 3, 4 C 5 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2 G 7 0, 0, 0, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3 T 10 1, 2, 2, 2, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5
Tbwt = T [...] double-stranded DNA again we get a memory usage of
app: |Σ| · n · 1 8 bytes ≈ 3.1 Gbytes
occ: |Σ| · n · 4 r ·k bytes ≈ 0.4 Gbytes
≈ 3.5 Gbytes.
References
[1] M. Burrows and D. Wheeler. A block-sorting lossless [...] takes m iteratiorns.
Bioinformatics context Backward search is widely used in read mappers like BWA [3]. Either searching for exact seeds or error-tolerant alignment is possible. Since double-stranded DNA …