Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/thesecondfox/skill/bio-database-access-sequence-similaritynpx skills add thesecondfox/skill --skill bio-database-access-sequence-similaritygit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-sequence-similarity)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-sequence-similarity"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-sequence-similarity.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00060 | $0.02511 |
| Opus 5 | $0.00030 | $0.01256 |
| Sonnet 5 | $0.00012 | $0.00502 |
| Haiku 4.5 | $0.00006 | $0.00251 |
Grade A, and why
bio-sequence-similarity scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz How it starts
The opening of the file, as written. The whole thing — 339 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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 <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Sequence Similarity Searches
Advanced methods for finding homologous sequences beyond standard BLAST.
"Find distant homologs" → Use iterative search (PSI-BLAST) or profile HMMs (HMMER) to detect remote sequence similarity that standard BLAST misses.
- CLI:
psiblast -query seq.fa -db nr -num_iterations 3orhmmsearch profile.hmm seqdb - Python:
NcbipsiblastCommandline()(BioPython)
PSI-BLAST (Position-Specific Iterated BLAST)
Builds a position-specific scoring matrix (PSSM) through iterations to find distant homologs.
Basic PSI-BLAST
psiblast -query protein.fasta -db nr -out results.txt -num_iterations 3
Save PSSM for Reuse
psiblast -query protein.fasta -db nr \
-out results.txt \
-out_pssm pssm.asn \
-out_ascii_pssm pssm.txt \
-num_iterations 5
Use Existing PSSM
psiblast -in_pssm pssm.asn -db nr -out results.txt
Output Format
psiblast -query protein.fasta -db nr \
-out results.txt \
-outfmt 6 \
-num_iterations 3 \
-inclusion_ethresh 0.001
Key Parameters
psiblast -query protein.fasta -db nr \
-num_iterations 5 \
-inclusion_ethresh 0.001 \
-evalue 0.01 \
-num_threads 8 \
-out results.txt
PSI-BLAST Parameters
| Parameter | Default | Description |
|---|---|---|
| -num_iterations | 1 | Number of iterations |
| -inclusion_ethresh | 0.002 | E-value for PSSM inclusion |
| -evalue | 10 | E-value threshold for reporting |
| -num_threads | 1 | CPU threads |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago First seen · 339 lines · 60 tokens per session scan A cb79e7cf6b25
bio-sequence-similarity is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 60 tokens to every session and 2,511 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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