| name | alterlab-blast |
| description | Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite. |
| license | MIT |
| allowed-tools | Read Write Edit Bash(python:*) Bash(makeblastdb:*) Bash(blastn:*) Bash(blastp:*) Bash(blastx:*) Bash(tblastn:*) Bash(blastdbcmd:*) Bash(diamond:*) |
| compatibility | Requires NCBI BLAST+ 2.17.0 binaries on PATH (conda: `bioconda::blast`; or Homebrew `blast`); no API key or account needed for local searches. DIAMOND (`bioconda::diamond`) is optional and only used for the large-protein fast path. Parsing/QC helper runs under `uv run python` with the standard library only. |
| metadata | {"skill-author":"AlterLab","version":"1.0.0"} |
BLAST+ — Command-Line Sequence Search
Run local NCBI BLAST+ 2.17.0 searches end-to-end: build a database with
makeblastdb, search it with blastn / blastp / blastx / tblastn, emit
machine-parseable tabular output, and scope by taxonomy. For very large protein
searches, hand off to DIAMOND blastp --ultra-sensitive (100x–10,000x the
speed of BLAST, per the DIAMOND project). This is the CLI / local-database
skill; it is deliberately distinct from the Biopython web API and the gget
one-liner (see routing table below).
Bulk DB builds and large searches are CPU/IO-heavy and fully offline — good
candidates to run on local compute rather than burning API calls.
When to Use This Skill
Use this skill when the request involves any of:
- "BLAST these sequences", "run blastn/blastp/blastx/tblastn", "command-line BLAST"
- "build a local BLAST database", "makeblastdb", "index this FASTA for BLAST"
- "search my reads against a local nt/nr database", "get tabular BLAST hits I can parse"
- "scope the BLAST search to a taxon" (
-taxids / -negative_taxids)
- "BLAST is too slow on millions of proteins" → DIAMOND
blastp
- retrieving sequences out of a BLAST DB (
blastdbcmd, requires -parse_seqids)
Does NOT Trigger
Route adjacent requests to the right sibling skill instead of forcing BLAST+:
| The request is really about… | Route to |
|---|
The web BLAST API (Bio.Blast.NCBIWWW.qblast), or scripting BLAST inside a Python pipeline with Bio.Blast parsing | alterlab-biopython |
A quick one-liner BLAST/database lookup (gget blast, gene/structure/enrichment lookups) | alterlab-gget |
| Unified programmatic access to many bio web services (UniProt, KEGG, Ensembl REST, NCBI eUtils) | alterlab-bioservices |
| Building/searching a phylogenetic tree from sequences, not a similarity search | alterlab-phylogenetics |
