skills.rest
mims-harvard
mims-harvardOFFICIAL
Explore all skills by this author →
Website𝕏@marinkazitnikGitHub

tooluniverse-sequence-analysis

Retrieve and analyze gene and protein sequences from NCBI, Ensembl, and UniProt databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#bioinformatics#sequence analysis#orthologs#Ensembl#uniprot#NCBI#fastq
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-sequence-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-sequence-analysis
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-sequence-analysis
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-sequence-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

It eliminates error-prone manual work in biological sequence analysis by providing verified workflows for fetching gene, transcript, and protein sequences, resolving gene identifiers across databases, and computing sequence statistics without guessing from memory.

Core Features & Use Cases

  • Sequence Retrieval: Fetch nucleotide and protein sequences from NCBI, Ensembl, and UniProt with correct parameter usage and fallback recipes for each database.
  • Ortholog and Domain Analysis: Discover orthologs across species, annotate protein domains via InterPro and Pfam, and run BLAST homology searches.
  • FASTQ QC and Alignment Support: Correctly interpret Trimmomatic paired-end counters and compute coverage depth with samtools for read alignment workflows.
  • Bundled Computation Scripts: Deterministic scripts for residue counting, GC content, reverse complement, codon tables, wobble pairing, and biology fact lookup.
  • Use Case: Given a question like "how many cysteines are in the TM3-TM4 linker of UniProt P24046", the skill fetches the sequence, extracts the region, and counts residues with a tested script instead of manual estimation.

Quick Start

Ask the agent to fetch the mRNA sequence for a human gene such as BRCA1 and it will resolve the gene ID, retrieve the accession, and return the FASTA sequence.

Frequently Asked Questions about tooluniverse-sequence-analysis

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

FAQPage Schema
How do I get the mRNA sequence for a human gene like BRCA1?▼

Search NCBI nucleotide with the gene name and organism filter, convert the returned UIDs to accessions with NCBI_fetch_accessions, then call NCBI_get_sequence with the accession and FASTA format. The skill documents this exact three-step recipe.

How do I find orthologs of a gene across species?▼

Use NCBIDatasets_get_orthologs with the numeric NCBI Gene ID, or EnsemblCompara_get_orthologues which accepts gene symbols directly. Resolve the gene symbol to a numeric ID first via NCBIGene_search if using the NCBI route.

Why does my Trimmomatic discarded read count look too low?▼

The Dropped field counts read pairs, not individual reads. Reads completely discarded equals Forward_Only plus Reverse_Only plus two times Dropped, summed across all samples. Reporting Dropped alone underestimates by roughly 100-fold.

How do I count residues in a specific protein region from UniProt?▼

Run the bundled sequence_tools.py script with count_region mode, passing the UniProt accession and 1-based start and end positions. It fetches the sequence live from the UniProt REST API and counts the residue programmatically.

What are the limitations of Ensembl sequence retrieval by gene ID?▼

Requesting CDS, cDNA, or protein sequences with a gene-level ENSG ID requires setting multiple_sequences to true, since genes have multiple transcripts. For a specific isoform, use a transcript ID such as ENST instead.

Related Skills

Explore More Education & Research Skills→
mims-harvardmims-harvard
1.6k

tooluniverse-sequence-retrieval

Retrieve and consolidate biological sequences across public databases with cross-references.

Official
Intermediate
itallstartedwithaideaitallstartedwithaidea
31

bioinformatics

Run Scanpy single-cell RNA-seq pipelines and pathway enrichment analyses.

Community
Advanced
ammawlaammawla
26

cross-reference

Link ENCODE genomic experiments to PubMed, ClinVar, GWAS Catalog, GTEx, and Ensembl.

Community
Advanced
jaechang-hitsjaechang-hits
298

biopython-molecular-biology

Parse FASTA, GenBank, and PDB files with Biopython for sequence analysis.

Community
Advanced