Discovery: NCBI BLASTAlign Search Space Is Not Fixed¶
Motivation¶
Precise sharded BLAST needs every shard to use the same statistical search space
as the full/reference run. We needed to test whether NCBI Web BLASTAlign uses a
fixed hidden searchsp for custom subject databases.
User-Facing Change¶
- Added docs/research/blast-searchsp-discovery.md, a
reproducible discovery note explaining how Web/default
searchspwas inferred. - Added scripts/dev/ncbi-searchsp-discovery.py, a manual dev probe that submits small NCBI Web BLASTAlign jobs and compares them with local BLAST+ runs through the terminal image.
API / IaC Diff Summary¶
- No API route changes.
- No frontend changes.
- No IaC changes.
Validation Evidence¶
Manual Web BLASTAlign + local BLAST+ probes on 2026-05-16:
| Case | RID | Inferred searchsp |
Local default equals Web | Local explicit -searchsp equals Web |
|---|---|---|---|---|
baseline_32nt_4_subjects |
0G0J7RM8114 |
2704 | yes | yes |
longer_64nt_4_subjects |
0G0PF0XD114 |
12544 | yes | yes |
wider_32nt_8_subjects |
0G0US0KB114 |
4950 | yes | yes |
Conclusion: the value is data/options dependent, not fixed.