Plant Pathogen Transcript Assemblies

The clustering of ESTs and construction of plant pathogen transcript assemblies (TAs) is very similar to the DFCI/TIGR gene indices. Both of them use the TGI clustering tools (available at http://compbio.dfci.harvard.edu/tgi/software/)for the sequence screen and cleaning, cluster, and assembly. However, there are several differences to be highlighted here:

  1. TAs are the assemblies of the expressed sequences from dbEST (EST) and GenBank (cDNA), and those "virtual" transcript sequences derived from genomic sequences are excluded.
  2. The TA clusters are assembled into the consensus sequences by the program CAP3 rather than Paracel Transcript Assembler.
  3. More stringent criteria are applied in the construction of TAs: 50 bp minimum match, 95% minimum identity in the overlap region, 20 bp maximum unmatched overhang.

Plant pathogen TA identifiers are of the form TA#_####, where # is the number of the transcript assembly and _#### represents the taxon id from NCBI

Plant Pathogen Transcript Assemblies Overview

Navigate the tree below to locate your species of interest. Select the plant transcript assembly statistics you would like displayed by clicking on a checkbox and clicking 'Display'. Checking a node will automatically select all the children. Not selecting a node will search the entire database as default.

The Current Release page displays all of the plant pathogen TA information in one view.

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