bio-local-blast
Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.
npx skills add BioTender-max/awesome-bio-agent-skills --skill local-blast --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: NCBI BLAST+ 2.15+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `blastn -version` then `blastn -help` to confirm flags - CLI: `makeblastdb -help` to confirm database build options If a flag is unrecognized or behavior changes, introspect with `-help` and adapt the example to match the installed version rather than retrying. # Local BLAST **"Run BLAST locally for speed and control"** -> Build or download a BLAST+ database, run the appropriate program with carefully chosen `-task`, masking, and thread settings, parse tabular output. Local BLAST is the right tool when remote is rate-limited or when the database must be reproducible (frozen). The biggest mistakes are (a) using `nt`/`nr` without realizing they're >250 GB and grow weekly, (b) not building with `-parse_seqids` and then being unable to extract hit sequences with `blastdbcmd`, (c) using default `blastn` for cross-species when `dc-megablast` is correct, and (d) thinking `-num_threads 32` will scale -- past ~16 threads BLAST is I/O bound. - CLI: `makeblastdb`, `blastn`/`blastp`, `blastdbcmd`, `update_blastdb.pl` (NCBI BLAST+) -
- Version Compatibility
- Installation
- Database format: v5 vs v4
- makeblastdb flag taxonomy
- -task taxonomy (the most-misused BLAST setting)
- Soft vs hard masking
- Thread scaling
- Output format reference (-outfmt)
- Prebuilt NCBI databases via updateblastdb.pl
- Code patterns
- Build and search a custom protein database
- Cross-species DNA with dc-megablast
- Short primer search
- Taxonomy-filtered search (BLAST v5 only)
conda (preferred) conda install -c bioconda blast macOS brew install blast Ubuntu sudo apt install ncbi-blast+ Verify blastn -version # NCBI BLAST+ 2.15+ expected update_blastdb.pl --showall pretty | head makeblastdb -in reference.fasta -dbtype nucl \
What does the bio-local-blast skill do?
Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill local-blast --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.