User Help Documentation

Welcome to the Maize Pangenome Database help guide. This documentation will help you navigate and utilize all features of our database effectively.

Welcome to Maize Pangenome Database

The Maize Pangenome Database is a comprehensive genomics resource platform built by the Crop Science and Genomics Innovation Center, South China Agricultural University. It integrates high-quality genome sequences from 24 maize varieties.

Database Overview
  • 24 Maize Varieties - Complete genome collections
  • 68.5 GB - Total genome data size
  • 892K Genes - Comprehensive gene annotation
  • 45.2M Variants - Genetic variations identified
  • Multiple Annotations - GO, KEGG, Pfam
  • Comparative Analysis - Orthogroup and synteny
Navigation Guide
  • Use the sidebar menu to navigate between different sections
  • Click on menu items to access main features
  • Use the search box in data tables to quickly find specific information
  • Access Quick Access links from the homepage for direct navigation

Browse Maize Varieties and Genes

Access comprehensive information about 24 maize varieties and their genomic data.

How to Use
  1. Navigate to Gene Search & Browse from the menu or homepage
  2. Browse the table showing all maize samples (varieties)
  3. Use the search box to filter by ID, Class, or Name
  4. Click the MORE button to view detailed sample information
Available Features
Sample List

View all 24 maize varieties with basic information

Detailed Information

Access comprehensive metadata for each sample

Data Export

Use the export buttons in the table to:

  • 📋 COPY - Copy table data to clipboard
  • 📄 Export to CSV - Download data as CSV file
Tip: You can adjust the number of rows displayed per page using the dropdown menu above the table.

Comprehensive Gene Annotation

Explore gene functional annotations from multiple databases including GO, KEGG, and Pfam.

GO Annotation (Gene Ontology)

Browse genes with Gene Ontology annotations including molecular function, biological process, and cellular component.

  • Gene ID - Unique identifier for each gene
  • EIL/EVM Gene ID - Alternative gene identifiers
  • Location - Chromosome, start, end position, and strand
  • GO Terms - Functional annotation from GO database
  • Association - View detailed gene association data
KEGG Annotation

Access pathway information and explore metabolic and signaling pathways.

Pfam Annotation

Browse protein families and domain architectures for all annotated genes.

Gene Association

Click the Association button to view:

  • Complete gene information (EIL ID, EVM ID, location)
  • All associated GO annotations with descriptions
  • KEGG pathway annotations
  • Pfam protein domain annotations
Strand Information: Forward (+) indicates the gene is on the forward strand, Reverse (-) indicates the reverse strand.

Comparative Genomics Tools

Perform comparative analysis across multiple maize varieties using orthogroup data.

What are Orthogroups?

Orthogroups are groups of genes that are descended from a single gene in the last common ancestor of the species being considered. They help identify:

  • Orthologs - Genes in different species that evolved from a common ancestral gene
  • Paralogs - Genes related by duplication within a genome
  • Gene families - Groups of related genes across multiple species
How to Use
  1. Access Genome Comparison Analysis from the menu
  2. Browse the orthogroup table showing all genes and their relationships
  3. Search by Orthogroup ID, Sample name, or Gene ID
  4. Export data for further analysis
Table Columns
Column Description
Orthogroup Unique orthogroup identifier (e.g., OG0000001)
Class Gene family or functional category
Sample Maize variety name
Gene Associated gene identifier
Note: This data is essential for understanding gene evolution, identifying conserved genes, and discovering species-specific genes.

Download Genomic Data

Access and download various genomic data files from our FTP server.

Available Data Types
Genome Sequences

Complete genomic sequences for all varieties

Annotation Files

Gene annotations in GFF/GFF3 format

Variation Data

SNPs and structural variants

Analysis Results

Orthogroup and synteny analysis data

How to Download
  1. Go to Data Download Center from the menu or homepage
  2. Browse the FTP server directory structure in the embedded viewer
  3. Navigate to the desired data folder
  4. Click on files to download them directly
  5. Or click Open in New Tab to open FTP server in a new window
Tip: For large file downloads, we recommend using a download manager or FTP client for better stability and resume capability.
Need Help?

If you encounter any issues downloading data or need assistance with specific file formats, please visit our Help page or Contact Us.

Getting the Most Out of Data Tables

All data tables in our database use DataTables with powerful features for data exploration.

Search and Filter
  • Global Search - Use the search box at the top right to filter all columns
  • Column Sort - Click column headers to sort ascending/descending
  • Pagination - Navigate through pages using pagination controls
Page Length

Adjust the number of rows displayed per page:

  • Click the dropdown menu showing "10" (default)
  • Select from options: 10, 20, 50, 100, 200, 500, 1000, etc.
  • Choose "All" to display all records on one page
Export Data

Use the export buttons in the top-right of each table:

  • 📋 COPY - Copy selected data to clipboard
  • 📄 Export to CSV - Download as CSV spreadsheet file
Performance Tip: For large datasets, we recommend using search filters before exporting to get specific data you need.

Frequently Asked Questions
How do I search for a specific gene?

Use the search box in any data table. You can search by Gene ID, chromosome, position, or annotation terms. The search filters data in real-time across all columns.

What file formats are available for download?

We provide data in various formats including FASTA (sequences), GFF/GFF3 (annotations), CSV (tabular data), and VCF (variants). Specific formats depend on the data type.

Can I compare genes across different maize varieties?

Yes! Use the "Genome Comparison Analysis" feature to view orthogroups. This shows how genes are related across all 24 maize varieties in our database.

What does the strand information mean?

Forward (+) indicates the gene is on the forward DNA strand, Reverse (-) indicates it's on the reverse strand. This is important for understanding gene orientation.

Troubleshooting
Table not loading or displaying data
  • Check your internet connection
  • Try refreshing the page (F5 or Ctrl+R)
  • Clear your browser cache
  • Ensure JavaScript is enabled in your browser
Download is slow or fails
  • Large files may take time to download depending on your connection
  • Try using "Open in New Tab" to access FTP directly
  • Use a download manager for better stability
  • Contact us if the issue persists
Search not returning expected results
  • Check for typos in your search term
  • Try using partial matches (e.g., "EIL" instead of full ID)
  • Clear the search box and enter a new term
  • Verify that the data exists in the database
Still Need Help?

If you can't find the answer to your question or need further assistance, please don't hesitate to reach out to our team.

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