Help Guide

Use the database for sample, gene, pangenome, and tool workflows

This guide summarizes the major database modules, table behavior, download workflow, and common troubleshooting steps for maize pangenome data exploration.

Sample List Gene Function Contact
Maize Pangenome Database
Quick Start

Common entry points

Sample Info

Browse metadata and open phylogenetic placement for maize samples.

List Tree

Gene Annotation

Search functional annotations, structures, TE records, and synteny.

Function Synteny

Pan-Genome

Explore pan-allele and pan-transcriptome relationships.

Allele Transcript

Tools

Use BLAST, JBrowse, tag conversion, and DL reannotation pages.

BLAST JBrowse
Documentation

Module guide

Use the sidebar to move between major modules. Data tables support server-side search, pagination, sorting, and export buttons on pages where export is enabled.

  • Start from Sample Info when selecting materials or populations.
  • Use Gene Annotation when the target is a gene, locus, or functional term.
  • Use Pan-Genome views when comparing allelic or transcriptomic relationships.
  • Use Download for public files and Tools for browser-based analysis.

The Gene Annotation module provides function, structure, TE annotation, and synteny views. Search by gene identifiers, annotation terms, location fields, or related metadata where supported.

  • Use Gene Function for GO, KEGG, Pfam, and association details.
  • Use Gene Structure to inspect structure data by sample.
  • Use Synteny to explore conserved gene groups and genomic context.

Pan-genome views help compare genes and transcripts across maize samples. Orthogroup records can be searched by orthogroup identifier, sample name, or gene identifier.

  • Use Pan-Allele for allelic relationship exploration.
  • Use Pan-Transcriptome for transcript-level comparison.
  • Export filtered tables when downstream analysis requires a subset.

Downloadable resources are available through the FTP browser. For large files, open the FTP server in a new tab and use a stable connection or download manager.

  • Use global search boxes in tables to narrow records before export.
  • Click table headers to sort supported columns.
  • Adjust page length to control how many rows are displayed.

  • If a table does not load, refresh the page and confirm JavaScript is enabled.
  • If search does not return results, try partial identifiers or broader terms.
  • If download is slow, open the FTP server directly and retry with a download manager.
  • If a data question remains unresolved, use the Contact page to reach the project team.
Support

Still need help?

Contact the database team for unresolved data access, usage, or technical questions.

Contact Us About Project