Alignment
3 problems from Rosalind — Bioinformatics Armory. Press Run on any block to execute it in your browser.
NEED — Pairwise Global Alignment
solved Problem statement
Calls NCBI, so it needs a network connection and its answer can change over time.
Reproduces the EMBOSS Needle score of 257 using align() with affine gaps (match 5, mismatch -4, gap_open -9, gap_extend -1). Asserted, but excluded from the hermetic CI gate because it fetches from NCBI.
SUBO — Suboptimal Local Alignment
solved Problem statement
Brute-force O(n^3) window scan; ~25 s. A motif-index approach would be the natural follow-up.
CLUS — Global Multiple Alignment
solved Problem statement