bio-local-blast

80 / 100 · Low risk

Fine to try.

By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18

Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

Works with any agent that supports SKILL.md skills.

Partially scanned — some files couldn't be read; we'll retry on the next scan

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 12 places.

skills/bioskills/local-blast/SKILL.md, line 32conda install -c bioconda blast
skills/bioskills/local-blast/SKILL.md, line 73makeblastdb -in reference.fasta -dbtype nucl \
skills/bioskills/local-blast/SKILL.md, line 136blastn -query q.fa -db db -outfmt "6 qseqid sseqid pident length qcovs qcovhsp evalue bitscore staxids sscinames stitle"

Show 9 more

skills/bioskills/local-blast/SKILL.md, line 149update_blastdb.pl --showall pretty | grep -E 'refseq|swissprot|nt|nr'
skills/bioskills/local-blast/SKILL.md, line 183REF=reference_proteins.fasta
skills/bioskills/local-blast/SKILL.md, line 207blastn -query mouse_cdna.fa -db human_refseq_rna \
skills/bioskills/local-blast/SKILL.md, line 219blastn -query primers.fa -db genome_db \
skills/bioskills/local-blast/SKILL.md, line 231blastp -query query.fa -db nr \
skills/bioskills/local-blast/SKILL.md, line 245cut -f2 top_hit_per_query.tsv | sort -u > hit_accessions.txt
skills/bioskills/local-blast/SKILL.md, line 257blastp -query A.fa -db B_db -outfmt 6 -evalue 1e-5 -num_threads 8 \
skills/bioskills/local-blast/SKILL.md, line 280out = subprocess.run([name, '-version'], capture_output=True, text=True)
skills/bioskills/local-blast/SKILL.md, line 291subprocess.run(cmd, check=True)

Downloads and installs other software

The author does not mention this.

Found in 2 places.

skills/bioskills/local-blast/SKILL.md, line 35brew install blast
skills/bioskills/local-blast/SKILL.md, line 38sudo apt install ncbi-blast+

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-local-blast' ] || [ -L ~/.agents/skills/'bio-local-blast' ]; then echo 'A skill folder named bio-local-blast already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/local-blast' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/local-blast' ~/.agents/skills/'bio-local-blast' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-local-blast' ~/.claude/skills/'bio-local-blast' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-07	`8cbdd18`	100