Search - Overview

PlantGDB downloads all Viridiplantae plant sequence data (GenBank and UniProt) every 4 months, parses them by species and makes data available for search, download or BLAST.

Current PlantGDDB Version: Release 187  [2011-12-15] (click for details...)

Search and Download Options

  • Quick Search (see header box)
  • Species Search/Download -- identify and retrieve sequences from any species PlantGDB's Public Plant Sequence repository.
  • ID or Keyword Search -- identify specific sequences by ID or annotation keyword.
  • FTP server -- batch download of sequences and PUT assemblies by species or sequence type.
  • TableMaker tool -- for complex PlantGDB database queries.

See below for more details.

Quick Search

For a quick search by ID or keyword, use the Search box near the PlantGDB logo at the top of any PlantGDB page. Additional search options are detailed below and can be accessed from the menu at left.

Species Search/Download

If you are interested in downloading all sequences from a given species (such as all maize sequences), you can access those data through our Species Search tool!

Id or Keyword Search

Navigate to the "ID or Keyword" Search Tool, and select "Sequence Id" or "Functional Annotation" from the dropdown. For Sequence ID, enter the gi, accession, GSS or PUT ID and click "Search". Any record (public or PlantGDB-specific) currently stored at PlantGDB can be retrieved by this method. For keyword search (e.g. Functional Annotation), type a word or phrase into the search box, click the button, and a list of sequence records that contain the word(s) will be returned. For example, a search for myb will retrieve a list of various PUT assembly containing a match to the myb keyword based on BLAST homology to UniProt.

FTP Server

Use the FTP Server to download public plant sequence data by GenBank sequence type (e.g. EST, GST, HTC) and/or by Genus / species.

TableMaker Tool

Although the Keyword Search can return a list of records, you might wish to find something more specific than just a list! You may want a simple two-column table, with one column displaying "Sequence ID" and the other displaying "Organism" to indicate the source of the sequence. Or you might need a more complex table with columns "Sequence ID", "Organism", "Tissue Type", and "Developmental Stage". The TableMaker tool allows you to specify search criteria for different columns, and allows you to select which columns to incorporate into a final report table. This enables you to create flexible queries such as "Show me all the maize ESTs from X library name and Y tissue type".

Search Genomes

The xGDB genome browsers provide both simple and advanced search capabilities. You can query either genomic segments and aligned sequence. Navigate to the xGDB Browser Home Page and click "Search" on the left menu, or enter an ID in the search box in the top menu.

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