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Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
PubMed Database workflow skill. Use this skill when the user needs Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API impleme...
Biopython: Computational Molecular Biology in Python workflow skill. Use this skill when the user needs Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinfor...
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopytho...
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Predict neoantigens that may be recognized by the immune system based.
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, or generating bootstrap consensus trees.
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