PlantGDB Tools
Select a tool from the menu at left or below. Also below are brief descriptions of each tool, with Help/Tutorial links and additional details (Click "More info...").
BioExtract Server
BioExtract harnesses the power of online informatics tools for creating and customizing workflows. Users can query online sequence data, analyze it using a broad array of informatics tools (web service or desktop), create and share custom workflows for repeated analysis, and save the resulting data and workflows in standardized reports. Help pages are available.
BLAST
PlantGDB implements the standard NCBI BLAST as its search engine. Search against single or multiple BLAST databases simultaneously. Up to 100 query sequences can be submitted in batch mode. A tutorial is available.
DAS
The Distributed Annotation System (DAS) server at PlantGDB allows remote genome browsers to access PlantGDB annotations.
FindPrimers
FindPrimers is a tool for identifying PCR primers for Ds transposon insertions in maize using the Primer3 program.
GeneSeqer
GeneSeqer produces plant gene structure models based on spliced alignment to genomic sequences of both native and homologous ESTs, cDNAs and protein sequences. A tutorial is available.
A parallel processor version of GeneSeqer is now available for larger runs (greater than 500 kb).
GenomeThreader
GenomeThreader produces plant gene structure models based on spliced alignment to genomic sequences of both native and homologous ESTs, cDNAs and protein sequences.
MuSeqBox
MuSeqBox is a program designed for examining multi-query sequence BLAST output (precomputed or user-input). MuSeqBox extracts the informative parameters of BLAST hits, saves them in tabular form in either text or HTML format, and will filter BLAST hits according to user-specified criteria. Help pages are available.
PatternSearch
Patternsearch searches patterns in genome sequence, ie. short matches possibly interspersed with mismatches and indels.
ProbeMatch
ProbeMatch allows the user to query your sequence against PLEXdb Probe Sequences. Use this tool to match your sequence(s) against the probe sequences by the Vmatch technology. The result will tell you if there is a match and where the match occurs.
TableMaker
The TableMaker tool can query PlantGDB's Plant Sequence database with an easy-to use GUI interface.
TE Nest
TE Nest is an annotation and visualization tool for the identification transposable elements in genomic sequence. TE nest is unique in that it reconstructs transposable elements separated by nesting of subsequent insertions and generates both annotation files and an svg graphic representation of element insertions. Help pages are available.
Tracembler
Tracembler allows the user to perform chromosome walks using trace sequences directly from NCBI's Trace Archive. This enables you to find your genes of interest in the most recent, pre-assembled sequence data from any species. Help pages are available.