bio-blast-searches
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
npx skills add BioTender-max/awesome-bio-agent-skills --skill blast-searches --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: BioPython 1.83+, NCBI BLAST+ 2.15+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show biopython` then `help(Bio.Blast.NCBIWWW.qblast)` to check signatures - CLI: `blastn -version` then `blastn -help` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # BLAST Searches (Remote) **"Find similar sequences in NCBI's database"** -> Submit a query to NCBI's remote BLAST servers; receive a Request ID (RID); poll for completion; parse the XML hit table. Best for one-off identification of a few sequences. For >50 sequences, switch to `local-blast` or DIAMOND/MMseqs2 in `remote-homology`. The two most consequential decisions: **which program** (defines query+target molecule types and word-size defaults) and **which database** (defines the search space and therefore E-value baselines). The third most important: do NOT misuse `max_target_seqs` -- it is an early-termination heuristic, not a "give me the top N hits" filter (Shah et al. 2019). - Python: `NCBIWWW.qblast(program, db, sequ
- Version Compatibility
- Required Setup
- Program decision (query vs database molecule)
- Database decision (search space)
- E-value interpretation (Karlin-Altschul)
- Composition-Based Statistics (CBS)
- The maxtargetseqs trap
- Word size, gap costs, and matrix
- RID lifecycle
- Code patterns
- Standard remote BLASTN with reproducible parameters
- Protein search with organism restriction
- Short peptide search
- Save XML for re-parsing
What does the bio-blast-searches skill do?
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill blast-searches --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.