lh3 / nasw Goto Github PK

git clone https://github.com/lh3/nasw
cd nasw && make
./nasw test/test-n.fa test/test-p.fa
./nasw test/DPP3-hs.gen.fa.gz test/DPP3-mm.pep.fa.gz

nasw provides a implementation of dynamic programming (DP) for protein-to-genome alignment with affine-gap penalty, splicing and frameshifts. The DP involves 6 states and 20 transitions, similar to the GeneWise model. Different from GeneWise, nasw explicitly implements the DP recursion with SSE2 or NEON intrinsics and is tens of times faster. Please see nasw.h for the brief API documentation.

1. The initial condition disallows gap opens at the beginning of the sequences.
2. Simplistic splice site model
3. The 32-bit mode uses excessive memory for traceback