PlantGDB Download Portal


Overview of our data update process

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...)

After each version update, PlantGDB's EST Assemblies are updated and annotated against UniProt sequences. At this time, any Genome Browsers requiring update will be refreshed with new sequence alignments.

It is our intent to make all of the PlantGDB raw and processed data, database tables, interface scripts, and analysis programs as freely and conveniently available as possible. Please contact us if you do not find what you need in our Download Portals. Options for download include

  • A comprehensive http Download Portal (sequence data by species, and MySQL databases); see below for details.
  • An ftp server (sequence data only).

Use menu at left to select a download option; see also Tips at right.

Sequence Download

  • Public Plant Sequence: Follow this link to specify other sequences you wish to download. Every 4 months, PlantGDB performs a download of all newly deposited plant DNA sequences available at the various NCBI databases (EST, PLN-RNA, GSS, HTC, HTG, STS, TSA, other genomic DNA sequences). Plant protein sequences are similarly obtained from UniProt. The extracted records are sorted by organisms to provide easy and fast access to individual species or to phylogenetically related subsets of organisms.
  • EST Assemblies: PlantGDB-derived unique transcripts (PUT) assembled from plant mRNA sequences available from GenBank (EST, PLN, HTC divisions). Also available are the actual assembly alignments, as well as the similar protein information annotated by BLASTX the unique transcript sequences against UniProt protein database. For more information on assembly, go to our EST assembly page.
  • GSS Assemblies: GSS contig sequences for the maize and sorghum Genome Surver Sequence (GSS) assemblies. For more information, go to our GSS assembly page.
  • Genomes: The 'xGDB' directory contains the data (genomic sequence, aligned transcript and protein sequence, gene models) from our genome browsers such as AtGDB, OsGDB, and ZmGDB. Follow this link to access data for each of these projects.
  • ASIP: ASIP contains the data for the Alternative Splicing in Plants project sub-folders AtTAG1 and RiceTAG1. Follow this link to access data for each of these folders.

Database Download

Databases and database structures are available for PlantGDB (GenBank and UniProt sequence) and all xGDB genome browsers (genomic sequence, aligned sequences, gene models.) From our Database Download Pages you can download and use these files to build and load your own local (MySQL) database.

  • Directories contain MySQL table structures (*.sql files) and table data (*.txt files) as generated by a MySQL "dump" command.
  • More information on PlantGDB's database structure can be found in the Help section (coming soon.)

Download via FTP

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

Tips for using the Download Portal:


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