Are there specific requirements for running BLAST jobs?

Yes, when running BLAST searches through NCBI, you must provide an email address as required by their web service policy for usage tracking.

What databases are supported by BioServices?

BioServices supports over 40 major bioinformatics databases, including UniProt, KEGG, ChEMBL, PubChem, Reactome, PDB, and QuickGO.

Can I use this skill for sequence alignment?

Yes, the skill includes built-in capabilities for running NCBI BLAST searches and sequence alignments (like MUSCLE) directly from your Python-based workflows.

How does BioServices handle biological identifier mapping?

It provides a unified interface to map identifiers across different biological resources, such as converting UniProt Accessions to KEGG gene IDs or Ensembl identifiers.

Does this skill support metabolic pathway analysis?

Absolutely. It can search for pathways by name, retrieve KEGG pathway data for specific genes, and extract structured protein-protein interaction networks.

BioServices Bioinformatics Toolkit

Name: BioServices Bioinformatics Toolkit
Author: lifangda

bylifangda

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Data Science & ML

Provides programmatic access to over 40 bioinformatics web services for biological data retrieval, identifier mapping, and pathway analysis.

About

BioServices is a comprehensive Python integration skill that enables Claude to interact with major biological databases like UniProt, KEGG, and ChEMBL through a unified API. It streamlines complex bioinformatics workflows by automating tasks such as sequence retrieval, cross-database identifier mapping, metabolic pathway discovery, and protein-protein interaction analysis. This skill is ideal for researchers and developers who need to integrate diverse biological data sources into automated analysis pipelines without manually navigating multiple web interfaces or managing disparate API protocols.

Key Features

Integrated sequence analysis and BLAST search job management
16 GitHub stars
Unified access to 40+ biological databases including UniProt, KEGG, and ChEMBL
Automated cross-database identifier mapping and conversion utilities
Metabolic pathway discovery and protein-protein interaction mapping
Support for both REST and SOAP/WSDL protocols within a single interface

Use Cases

Characterizing proteins by automatically retrieving sequences, annotations, and functional pathways
Mapping chemical compound IDs across different pharmacological and biological databases for drug discovery
Building automated pipelines for batch gene ontology (GO) term annotation and genomic data mining

About

Key Features

Integrated sequence analysis and BLAST search job management
16 GitHub stars
Unified access to 40+ biological databases including UniProt, KEGG, and ChEMBL
Automated cross-database identifier mapping and conversion utilities
Metabolic pathway discovery and protein-protein interaction mapping
Support for both REST and SOAP/WSDL protocols within a single interface

Use Cases

Characterizing proteins by automatically retrieving sequences, annotations, and functional pathways
Mapping chemical compound IDs across different pharmacological and biological databases for drug discovery
Building automated pipelines for batch gene ontology (GO) term annotation and genomic data mining