Blast Search Agent Skill

Run BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search. Triggers on "blast", "sequence similarity", "homology", "identify sequence".

573 tokens

context cost

the whole folder, loaded on every use

files

instructions only

copies elsewhere

how many repositories repackaged it

132

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill blast-search

The instruction itself

8 sections, as written by the author

BLAST Search

Run NCBI BLAST+ searches inside the BioClaw container.

When to Use

User provides a DNA/RNA/protein sequence and wants to find similar sequences
User asks to identify an unknown sequence
User wants to check sequence conservation across species

How to Execute

1. Determine BLAST program

| Input | Database | Program |

|-------|----------|---------|

| Nucleotide query | Nucleotide DB | blastn |

| Protein query | Protein DB | blastp |

| Nucleotide query | Protein DB | blastx |

| Protein query | Nucleotide DB | tblastn |

2. For local BLAST (sequences provided by user)

# Create query file
cat > /tmp/query.fa << 'EOF'
>query_sequence
ATGCGATCGATCGATCG...
EOF

# Create subject file (if user provides reference)
cat > /tmp/subject.fa << 'EOF'
>reference
ATGCGATCGATCGATCG...
EOF

# Run BLAST
blastn -query /tmp/query.fa -subject /tmp/subject.fa -outfmt 6 -evalue 1e-5

3. For remote BLAST (against NCBI databases)

Use BioPython's NCBIWWW module:

from Bio.Blast import NCBIWWW, NCBIXML
from Bio import SeqIO

# Read sequence
sequence = "ATGCGATCGATCGATCG..."

# Run remote BLAST
result_handle = NCBIWWW.qblast("blastn", "nt", sequence)
blast_records = NCBIXML.parse(result_handle)

for record in blast_records:
    for alignment in record.alignments[:10]:
        print(f"Title: {alignment.title}")
        for hsp in alignment.hsps:
            print(f"  Score: {hsp.score}, E-value: {hsp.expect}")
            print(f"  Identity: {hsp.identities}/{hsp.align_length} ({hsp.identities/hsp.align_length*100:.1f}%)")

4. Output format

Present results in a clear table:

*BLAST Results (top 10 hits)*

• Hit 1: Homo sapiens TP53 gene (98.5% identity, E=1e-45)
• Hit 2: Mus musculus Trp53 gene (89.2% identity, E=1e-38)
...

5. Follow-up suggestions

After showing results, suggest:

Multiple sequence alignment of top hits
Phylogenetic analysis
Domain/motif analysis of the query
Structural comparison if protein

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How to use it

Copy the folder

Take biotender-max/blast-search from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.