Frequently Asked Questions

PlantGDB provides sequence data for >70,000 plant species, custom EST assemblies (PUT) for over 150 species, web tools and plant genome browsers, as well as an outreach portal for plant genomics. For more information on PlantGDB, visit our About page or take a brief tour on our Help Home Page.

Use the 'feedback' link at the top right corner of any PlantGDB web page. We will contact you within 24 hours. You are also welcome to contact any of the PlantGDB contacts listed under About.

PlantGDB has been optimized for use with Firefox 3, Safari, or Internet Explorer 7 / 8. Many advanced features require that Javascript be enabled. If you encounter problems viewing any page at PlantGDB.org, please contact us using our feedback form. Please include a description of what didn't work as expected, and what web browser/operating system you were using. We will do our best to address the problem.

• PlantGDB's Public Plant Sequence data is updated every four months, coinciding with every other GenBank Version Release (December, April, and August). Transcript assemblies (PUT) are updated at this time and are typically made available 2-4 weeks after version update.
• Genome data at PlantGDB are updated periodically when a new genome assembly becomes available, or when transcript data are significantly increased.
• For more information , see FAQ categories 'Plant Sequence and PUT assemblies' and 'Genome Browsers' below.

• Sequence data and metadata data are stored on our servers in three primary forms: 1) In MySQL databases which store metadata and links to other data types; 2) In multiFASTA-formatted sequence files, for sequence retrieval using FASTACMD; 3) In indices for BLAST and GeneSeqer analysis.
• For more information about how to access and download PlantGDB sequence data, see FAQ categories 'Plant Sequence and PUT assemblies' and 'Genome Browsers' below.

PlantGDB's genome focus is on accurate spliced alignments of transcript to genomes, a critical component of accurate genome annotation. The xGDB genome browser platform used at PlantGDB has unique features that make it useful for viewing and annotating genomes:

• All splicing evidence can be viewed online and reproduced using web tools provided at PlantGDB.
• A community annotation tool (yrGATE) and gene model incongruence-detection system (GAEVAL) are built in, to facilitate genome annotation.
• Each xGDB has powerful BLAST tools and search tools to retrieve upstream sequence for motif analysis.
• xGDB supports the DAS (Distributed Annotation Service) standard for cross-platform data display, and provides both DAS client and DAS server capabilities.
• The complete xGDB code is available as open source software and can be custome-installed on a Linux server.

For more information, see the Genome Browser Help Page.

Likely reasons include: too large a region chosen; or region is very heavily annotated with one track type (typically, EST). In either case, the load on the graphics engine causes a long delay in track display times. Solutions:

• Re-enter a set of coordinates that span a narrower region and try again.
• If problem remains, try unselecting the EST track type using the track control and re-submit the region request.
• If you are unable to solve the problem, please contact us using the Feedback form, describing the region you were attempting to view.

DAS (Distributed Annotation Service) standard for cross-platform data display, and provides both DAS client and DAS server capabilities (coming soon).

For more information, see the Genome Browser Help Page.

PlantGDB downloads GenBank and UniProt sequence data approximately every four months, corresponding to every other GenBank Release. Sequence data is parsed according to a database schema, and individual sequence files are filtered to detect vector and repeat sequence. When you download FASTA-formatted sequence data from PlantGDB, you may see differences in the masking of repeat or vector regions, but the sequence is otherwise identical.

• PUT = PlantGDB-assembled Unique Transcript. PlantGDB regularly assembles transcript sequences (EST and cDNA) for species with >10,000 sequences in GenBank, as well as by request for smaller or combined datasets. The resulting sequence assemblies (PUTs) are made available for search, download, BLAST, and spliced alignment using GeneSeqer.
• PUT assemblies include both contigs (comprising multiple sequences) and singletons. They are named according to version number, genus_species, and sequence number.

For more information visit the EST Assembly Page (Home>Left Menu>EST Assembly).

You can download sequence for any plant species by going to the Download portal (Home>Download>Sequence). Enter Genus/species and click 'Search'. (For popular species, use the shortcut "Featured Species" on the Home Page left menubar.)

To download PUT assemblies, go to the EST contig Download portal (Home>EST Assembly>Download)

To download large datasets, visit our ftp site at ftp.plantgdb.org where you can download all PUT assemblies or plant sequences using ftp.

PlantGDB's sequence data is updated every 4 months, coinciding with every other GenBank Release (odd numbers). For example, recent updates included V.165 (April 2008) and V.163 (December 2007).

If you visit the Download page for any species, you can retrieve files named as:

• Genus_species.PUT_member.txt
• Genus_species.alignment.txt

Which both provide the mapping of the ESTs to a PUT.

Alternatively, from the "Search" page, e.g.

http://www.plantgdb.org/search/display/data.php?Seq_ID=PUT-157a-Oryza_sativa-6232

You can view or retrieve the EST components of an individual PUT

Return to top

PlantGDB's sequence data is updated every 4 months, coinciding with every other GenBank Release (odd numbers). For example, recent updates included V.165 (April 2008) and V.163 (December 2007).

PlantGDB's taxonomic conventions will always reflect NCBI's current naming system since our data source is GenBank. Check the current taxonomic name for your species using GenBank's Taxonomy browser. It is possible that the genus and/or species name has changed.

Return to top