Help & Documentation
Welcome to Maize Pangenome Database
This help guide will walk you through the main features and functionality of our database.
Navigation Basics
- Use the sidebar menu to navigate between different sections
- Click on menu items to expand sub-menus
- Use the search bar to quickly find specific information
Browsing Sample Data
The Sample Info section provides detailed information about maize samples in our database.
Available Features
- View complete sample metadata
- Search and filter samples by various criteria
- Export sample information in different formats
- Access detailed genomic information for each sample
Gene Annotation Databases
Our database provides comprehensive gene annotation information from multiple sources:
GO (Gene Ontology)
- Browse genes with GO annotations
- Filter by GO terms and categories
- View functional annotations and descriptions
KEGG (Kyoto Encyclopedia of Genes and Genomes)
- Access pathway information for genes
- Explore metabolic and signaling pathways
- View enzyme commission numbers
Pfam (Protein Families)
- Browse protein family annotations
- View domain architectures
- Access functional domain information
Expression Data
- View gene expression profiles
- Compare expression across different conditions
- Access quantitative expression data
Downloading Data
You can download various types of genomic data from our database:
Available Download Types
- Genome: Complete genomic sequences
- Annotation: Gene annotation files in GFF3 format
- CDS: Coding DNA sequences
- Protein (PEP): Protein sequences
- mRNA: Messenger RNA sequences
Download Instructions
- Navigate to the Download section
- Select the desired data type
- Choose the specific samples or datasets
- Click the download button
Integrated Analysis Tools
Our database provides various bioinformatics tools for data analysis:
Available Tools
- Blast: Sequence similarity search
- Gene ID Convert: Convert between different gene identifier formats
- Orthofinder: Orthology analysis
- SYN: Synteny analysis tools
- ShinySyn: Interactive synteny visualization
- Structure Variant: Structural variant analysis
- Haplotype: Haplotype analysis tools
- Pan-coding protein: Pangenome protein analysis
Common Issues and Solutions
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Still Need Help?
If you can't find the answer to your question, please don't hesitate to contact us.