biopython-sequence-analysis SKILL.md skillA
biopython-sequence-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/biopython-sequence-analysis@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/biopython-sequence-analysis/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 33,989 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Biopython: Sequence Analysis Toolkit ## Overview Biopython provides a comprehensive suite of modules for sequence-centric bioinformatics: reading and writing every major biological file format (FASTA, FASTQ, GenBank, GFF), querying NCBI databases programmatically, running BLAST searches and parsing results, aligning sequences pairwise or in multiple-sequence alignments, and building and visualizing phylogenetic trees. This skill focuses on analysis workflows — from NCBI data retrieval through alignment to phylogenetic inference. For PCR primer design, restriction enzyme digestion, cloning simulation, protein structure analysis (Bio.PDB), and molecular weight/Tm calculations, see **biopython-molecular-biology**. ## When to Use - Download a gene family from NCBI Nucleotide/Protein, align sequences, and construct a phylogenetic tree - Parse GenBank or GFF3 annotation files and extract CDS sequences for a set of features - Run a BLAST search against NCBI `nt` or `nr`, filter significant hits, and fetch their full sequences - Compute pairwise sequence identities or score alignments with BLOSUM62/PAM250 matrices …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/biopython-sequence-analysis@sha256:001695ab4739ab8fThe line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_wuxjksttkmlgigai)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 34 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 33,989 B | A | view · diff |
| git:20260414.65bebbb | 2026-04-14 | 65bebbb | 34,176 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 33,855 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (33989 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_wuxjksttkmlgigai GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/biopython-sequence-analysis GET https://markdownregistry.com/api/v1/blob/001695ab4739ab8f178b3033d86d5a9615d1cb6759f8b984875f89f1bc85f99a
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