Genomic Region Generator

The Genomic Region Generator extracts specific genomic regions (genes, exons, introns, UTRs, etc.) from reference genomes sourced from NCBI or Ensembl.
It supports flexible region selection, automatic file retrieval, and efficient caching to accelerate subsequent runs with identical parameters.

How it works

Select data source
- Choose between NCBI or Ensembl as your genome annotation source.
- Each source provides access to curated reference genomes and annotations for various species.
Configure source parameters
- For NCBI:
  - Taxon: Select the taxonomic group (e.g., Vertebrate Mammalian, Archaea, Bacteria, Fungi, Invertebrate, Plant, etc.)
  - Species: Choose a specific species from the selected taxon
  - Annotation Release: Pick the desired annotation version
- For Ensembl:
  - Species: Select from available Ensembl species
  - Annotation Release: Pick the desired release version
Select genomic regions
Choose one or more regions to extract:
- Gene: Full gene sequences including all features
- Intergenic: Sequences between genes
- Exon: Coding and non-coding exonic sequences
- UTR: Untranslated regions (5’ and 3’)
- CDS: Coding sequences only
- Intron: Intronic sequences
- Exon-Exon Junction: Splice junction sequences
  - If selected, specify the Block Size (number of nucleotides to include from each flanking exon)
Generate FASTA files
- When you submit a pipeline, the form data is sent with your request.
- The backend processes your request using a two-level caching mechanism (see Caching FASTA Files for details).
- Multiple region selections are handled in a single request, with each region combination cached independently.

Use cases

Probe design pipelines: Generate target and reference databases for ISH probe design
Custom sequence extraction: Extract specific genomic features for analysis
Multi-species workflows: Process annotations from different organisms in parallel
Version-controlled analyses: Use specific annotation releases for reproducible research