Search the Documentation
guidance for using PlantQTLdb, working with Assistant, understanding analysis methods and tracing data provenance
Getting Started
detailed guidance on PlantQTLdb features, gene and trait search, and evidence-page navigation
- Introduction to PlantQTLdb Understand how genes, traits, molecular phenotypes, QTLs, integrated analyses, and literature are connected.
- Searching for Genes and Traits Use direct search and the indexed catalogs to locate searchable genes and phenotype terms.
- Navigating Gene-Centered Results Move from the gene overview to molecular phenotypes, QTL evidence, and supporting literature.
- Using Trait–Gene Evidence Compare GWAS, TWAS, SMR, colocalization, and EWAS in one dataset–trait context.
PlantQTLdb Assistant
choose a mode, try copyable questions, and interpret tool results, charts and downloads
- Getting Started with Assistant create an account, choose a mode, and understand your results and daily allowances
- Gene Structure and Sequence Extraction view all annotated transcripts and extract reference DNA, cDNA, CDS, protein or promoter sequences
- Variant Annotation and Local QTL Evidence inspect gene-region variants, stored effect annotations and nearby QTL/GWAS evidence with downloadable tables
- Functional Enrichment with g:Profiler find over-represented functions in a gene set and understand adjusted P values and experimental backgrounds
- Network Analysis with STRING explore functional associations or physical interaction evidence between candidate proteins
- Finding Sequencing Data with ENA locate public sequencing runs and source records without downloading large read files
- Sequence Similarity Search with BLAST submit a short DNA or protein sequence to NCBI and retrieve its local-alignment results
- Plant Motif Analysis with JASPAR and FIMO find plant transcription-factor motifs and scan short DNA for predicted matches
- DNA Analysis with Evo2 score supplied DNA, compare matched substitutions or request a model-generated continuation
- External Biological Evidence Sources understand the protein, ontology, pathway, expression and literature sources used during evidence investigation
- Troubleshooting and Limitations resolve missing cards, unsupported inputs, pending jobs and incomplete results
Analysis Methods
understand the questions, reported statistics, thresholds and limitations of each method
Data
trace dataset origins, sample cohorts, phenotype availability and source publications
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