Skill UI

BioServices provides Python wrappers for 40+ bioinformatics services, allowing cross-database queries, identifier mapping, pathway exploration, and sequence or compound research within consistent workflows.

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

High-performance Rust toolkit with Python bindings for genomic interval analysis, covering overlap detection, coverage track generation, ML tokenization, reference sequence handling, fragment processing, and scoring workflows for sequencing datasets.

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

scikit-bio provides a Python-native biological data toolkit for reading/writing FASTA/Newick files, manipulating sequences, building alignments and phylogenies, and calculating diversity metrics for microbiome and ecology workflows.

Direct REST API access to UniProt for searching proteins, fetching FASTA sequences, mapping identifiers, selecting annotations, and streaming large datasets within Python workflows.

Query the JASPAR REST API and Python helpers to retrieve TF binding profiles, convert PFMs to PWMs, and scan DNA sequences for high-confidence motifs, enabling regulatory variant interpretation, ChIP/ATAC analysis, and TF network construction.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

This guide details how to write advanced correlation searches using Splunk's Search Processing Language (SPL). It covers techniques like threshold-based detection, sequence analysis, and anomaly detection to identify sophisticated security threats (e.g., brute force, data exfiltration, lateral movement) in a Security Operations Center (SOC) environment. Mastery of SPL is essential for closing SIEM detection gaps and ensuring compliance.

Provides direct REST API access to UniProt, the premier resource for protein sequence and functional information. This skill enables users to search proteins by name, gene, or accession number, retrieve sequences in FASTA format, perform cross-database ID mapping (e.g., Ensembl, RefSeq), and analyze functional annotations (GO terms) for building comprehensive bioinformatics pipelines.