alterlab-blast

# 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 BLA...