Available Features Explained

Welcome to the Available Features Explained section of the GenomeSet documentation. This section provides an in-depth explanation of every core function and feature available on the GenomeSet platform — from data uploading to advanced genomic analysis tools, result management, and data sharing.

Data Management Features

User Registration and Profiles

  • Create a personal account to access data upload, saving, and sharing features.
  • Manage personal information and security settings.
  • Access your uploaded files, saved projects, analysis results, and sequence subsets.

Upload Data

  • Upload your personal genomic data in FASTA (.fa/.fna/.fasta) or tabular (CSV/TSV) format.
  • Assign a data type during upload for proper parsing.
  • Uploaded files are stored under the Uploaded Files section in your profile.
  • Easily select and manage uploaded files for analysis using the Select button and buffer window.

Data Exploration Tools

Species Explorer

  • Browse a rich, interactive taxonomic tree of publicly available organisms from NCBI.
  • Select organisms by kingdom, division, class, order, or species.
  • Use checkboxes to select up to 5 organisms for comparative analysis.
  • Visualize organism lineages and navigate taxonomic relationships.
  • Selected organisms appear in a buffer for quick analysis or removal.

GEO Dataset Explorer

  • Search and browse publicly available gene expression datasets from the GEO (Gene Expression Omnibus) repository.
  • Select datasets based on study criteria or data type.
  • Analyze gene expression data using GenomeSet’s integrated tools.

Analysis Functions (Analyzer Page)

Once data or organisms are selected, the Analyzer Page becomes available. Here, you can run a wide array of genomic analyses.

Parsing & Sequence Type Selection

  • For NCBI organisms, the system downloads .fna (genomic sequences) and .gff3 (annotation) files.
  • Extracts specific regions: cDNA, CDS, UTR 5’, UTR 3’, and Gene sequences.
  • Checkboxes allow you to choose which sequence types to include in your analysis.

Core Analysis Functions

  • Length Analysis:

    Measures and visualizes sequence length distributions for selected regions.

  • GC-Content:

    Calculates the GC (Guanine + Cytosine) percentage for sequences or sequence regions.

  • CpG-Island Detection:

    Identifies high-density CpG regions — typically associated with gene regulation areas.

  • K-Mer Frequency Analysis:

    Counts and analyzes all possible k-length subsequences within genomic sequences.

Projects Tools

GFF3 Parser: Coming soon — parse and explore gene annotations.
Massive Genome Research Tool: Coming soon — analyze large genome batches.
Genomes Map: Future feature for visualizing genome structures interactively.