Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026
FreePublished on GitHub
blast-search
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".
The English summary is being prepared. Showing the original description.
Run score Not tested
See how to installFiles included (1)
- SKILL.md2.2 KB
SKILL.md (original)
Review the instructions the agent will receive before you install.
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
Reviews
No reviews yet. Tell others what you thought.
Comments
No login needed. Share how it worked for you, ask a question, or note where it did not run.
No comments yet. Be the first to write one.
More skills from this repository
alphafold
FreeValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026
AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm2-sequence-scoring. For QC thresholds, use protein-design-qc.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026
Workflow for event-level and isoform-level splicing analysis with sashimi-ready outputs and splice QC.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026
atac-seq
FreeATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026
bindcraft
FreeEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
The English summary is being prepared. Showing the original description.
BioTender-max/awesome-bio-agent-skills204Updated Jul 2, 2026