biopython-sequence-analysis

Name: biopython-sequence-analysis
Availability: InStock
Author: jaechang-hits

Perform sequence analysis with Biopython, including NCBI Entrez downloads and BLAST searches.

298|27|Updated Feb 18, 2026

Search Tags:#bioinformatics #alignment #sequence analysis #ncbi #biopython #phylogenetics #blast

Ready to run

npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill biopython-sequence-analysis

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: biopython-sequence-analysis
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/biopython-sequence-analysis
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill biopython-sequence-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, numpy, matplotlib, muscle, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill streamlines complex bioinformatics workflows by providing tools to fetch, analyze, and interpret biological sequence data from public databases and local files.

Core Features & Use Cases

Data Retrieval: Download sequences and annotations from NCBI databases (Entrez).
Sequence Analysis: Parse various file formats (FASTA, GenBank, GFF), perform alignments (pairwise, multiple), and build phylogenetic trees.
Similarity Search: Run BLAST searches locally or remotely to find homologous sequences.
Use Case: Analyze a gene family by downloading orthologs from NCBI, aligning them using MUSCLE, and constructing a phylogenetic tree to understand evolutionary relationships.

Quick Start

Fetch the GenBank record for NM_007294 and print its basic statistics.

Frequently Asked Questions about biopython-sequence-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I download sequences from NCBI using Biopython?▼

You can download sequences from NCBI using Biopython by utilizing the Entrez module to fetch records and annotations programmatically. This Skill facilitates retrieving data directly from NCBI databases for downstream analysis.

Can I run BLAST searches and perform multiple sequence alignment in one workflow?▼

Yes, you can run BLAST searches to find homologous sequences and perform multiple sequence alignment in one workflow. This Skill supports executing BLAST and aligning sequences using MUSCLE for comparative genomics.

What is the best way to build a phylogenetic tree from GenBank sequences?▼

The best way to build a phylogenetic tree from GenBank sequences is to parse the records, perform multiple sequence alignment, and construct the tree. This Skill enables constructing phylogenetic trees to analyze evolutionary relationships.

Does this Biopython Skill support parsing FASTA and GFF files for gene family studies?▼

Yes, this Biopython Skill supports parsing FASTA and GFF files for gene family studies. It handles various sequence formats including FASTA and GenBank, allowing you to extract data for comparative genomics analysis.

Do I need MUSCLE installed to perform multiple sequence alignment with Biopython?▼

Yes, you need MUSCLE installed to perform multiple sequence alignment with Biopython using this Skill. MUSCLE is a required dependency for executing the multiple sequence alignment operations within the workflow.

Why use Biopython for programmatic NCBI data retrieval instead of manual downloads?▼

Using Biopython for programmatic NCBI data retrieval automates fetching large datasets, overcoming the limitations of manual downloads. This Skill streamlines building data retrieval pipelines to efficiently gather orthologs and annotations.