Introduction

GenomeSet is a comprehensive genome analysis system for uploading personal data or exploring public organism genomes and GEO datasets. The platform enables extraction of sequence regions, comparative analysis, and visualization using flexible, user-friendly tools.

User Accounts and Profiles

Registering an account allows you to:

  • Upload and manage personal genomic files
  • Save and share projects and results
  • Store filtered sequence subsets
  • Access project history and results anytime

Your Profile Page includes:

  • Personal Information
  • Uploaded Files
  • Saved Projects
  • Analysis Results
  • Sequence Subsets

Uploading Data

Supported file types:

  • FASTA (.fna, .fa, .fasta)
  • Data tables in CSV / TSV format

Steps:

  1. Navigate to Start Analyzing → Upload Data.
  2. Choose your file.
  3. Select its type.
  4. Upload and view your files in the Uploaded Files section of your profile.
  5. Select files for analysis via the Select button.

Use the buffer window to:

  • Send selected files to the analyzer
  • Choose taxonomy for comparative analysis
  • Remove files from selection

Species Explorer

Features:

  • Interactive taxonomic table
  • Left-side taxonomic tree
  • Lineage navigation (from kingdom to species)

Process:

  1. Select organisms using checkboxes.
  2. Add to buffer.
  3. Review selected items at the top.
  4. Click Go to Analyzer to proceed.

GEO Dataset Explorer

Use public gene expression data from the Gene Expression Omnibus (GEO) database:

  • Explore available datasets
  • Select data by criteria
  • Analyze using GenomeSet’s built-in tools

Analyzer Page Overview

  1. Selected Objects Section

    • Displays selected files or organisms
    • System automatically downloads and parses genomic data for public organisms
    • Available sequence types (cDNA, CDS, UTR 5’, UTR 3’, Genes) displayed after parsing

  2. Analysis Functions Panel

    Located on the right:

    • Length
    • GC-Content
    • CpG-Island
    • K-Mers
    • Nucleotide frequencies
    • Sequence region IDs
    • Codon analyses (for CDS)
    • Amino acid analyses (for CDS)

  3. Results Panel

    Displays:

    • Graphical charts
    • Properties and filters
    • Data tables
    • Sequence region settings (limit to 0-100%)

  4. User Functions (Registered Users Only)

    • Save Project
    • Share Project
    • Save Result
    • Save Subsets

Saving and Managing Data

  • Save entire projects for later resumption
  • Share projects with other users
  • Save filtered result tables
  • Save subsets for future analysis
  • Use previously saved subsets in new projects

Additional Genomic Tools

Coming soon:

  • GFF3 Parser
  • Massive Genome Research Tool
  • Genome Maps and Visualizers

Tips, Best Practices, and Example Workflows

  • Compare CpG islands between multiple organisms
  • Analyze codon usage for a species or group
  • Focus analysis on specific genomic regions (e.g., UTRs only)
  • Save and reuse interesting subsets