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).

More info...

GenomeThreader

GenomeThreader produces plant gene structure models based on spliced alignment to genomic sequences of both native and homologous ESTs, cDNAs and protein sequences.

More info...

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.

yrGATE

yrGATE is a tool for community annotation of genomic sequence, used in conjunction with the xGDB genome browsers at PlantGDB. Help pages are available.

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