Energy Grass Database (EGDB) Documentation

Table of Contents

1. Home Module
2. Species Module
3. Tools Module
4. Search Module
5. Downloads Module
6. About Module

1. Home Module

1.1 News

• Latest updates and announcements in energy grass research
• Recent database updates and new features
• Conference and event information

1.2 External Links

• Links to related databases
• Research institution websites
• Collaboration networks

1.3 Publications

• Recent research papers
• Key references
• Database-related publications

2. Species Module

2.1 Browse

• Complete list of energy grass species
• Species information pages
• Taxonomic classification
• Image galleries

2.2 Germplasm

• Germplasm resources
• Genetic background information
• Source and availability
• Conservation status

2.3 Phenotype

• Morphological characteristics
• Growth parameters
• Stress tolerance data
• Biomass yield information

3. Tools Module

3.1 JBrowse / BLAST+

JBrowse

• Interactive genome browser
• Multiple track visualization
• Custom track upload
• Feature annotation display

BLAST+

• Multiple BLAST programs (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX)
• Custom database selection
• Parameter customization
• Results visualization

3.2 Primer3 / OrthoVenn3

Primer3

• PCR primer design
• Custom parameter settings
• Primer quality checking
• Batch design capability

OrthoVenn3

• Orthologous gene analysis
• Venn diagram visualization
• Protein cluster comparison
• GO enrichment analysis

3.3 TE Identification

• Transposable element detection
• TE family classification
• Distribution analysis
• Annotation tools

3.4 CRISPR / GWAS

CRISPR

• Guide RNA design
• Off-target prediction
• Efficiency scoring
• Vector design assistance

GWAS

• Genome-wide association analysis
• Phenotype-genotype correlation
• Statistical analysis tools
• Manhattan plot visualization

4. Search Module

4.1 Species Search

• Search by species name
• Filter by characteristics
• Geographic distribution
• Phenotypic traits

4.2 Gene Search

• Search by gene ID/name
• Sequence-based search
• Functional annotation
• Expression patterns

4.3 Gene Classification

• Gene family categorization
• Functional categories
• Pathway assignments
• Ontology information

4.4 Gene Expression

• Expression profiles
• Tissue-specific patterns
• Developmental stages
• Stress responses

4.5 TF Identification

• Transcription factor families
• Regulatory networks
• Binding site prediction
• Expression correlation

5. Downloads Module

5.1 Genome / GFF / CDS

• Complete genome sequences
• Gene feature format files
• Coding sequences
• Assembly statistics

5.2 Histone Modification

• ChIP-seq datasets
• Modification patterns
• Peak calling results
• Regulatory annotations

5.3 Chromatin Accessibility

• ATAC-seq data
• DNase-seq data
• Regulatory regions
• Chromatin states

5.4 TE Annotation

• Transposable element annotations
• TE family classifications
• Distribution patterns
• Integration sites

6. About Module

6.1 About Us

• Database introduction
• Development team
• Funding information
• Collaboration opportunities

6.2 Tutorial

• Step-by-step guides
• Video tutorials
• Tool demonstrations
• Example analyses

6.3 Guide

• User manual
• FAQ section
• Best practices
• Troubleshooting tips

Contact Information

• Technical Support & Database Feedback: ashelylinluo@126.com
• Website: https://engrass.juncaodb.cn

Citation

When using EGDB in your research, please cite: [Citation details]

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Last Updated: November 2024
Version: 1.0