PCD offers BLAST with sequence databases from the crops featured on the database (Fig. 24). Genome, unigene, and reference transcriptome assemblies are available along with model genome sequences from Medicago truncatula, Lotus japonicus, and Glycine max.
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Figure 24. Blast Tool homepage.
The Tripal BLAST interface (Fig. 25) looks and functions like the interface available on NCBI and information on the different settings and how to use BLAST can be found in the BLAST Help manual. Please note that one you initiate a job, you are taken to an unique results page that you can book mark and return to later.
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Figure 25. Tripal BLAST interface
The BLAST module displays the results in a interactive interface. At the very top are links to download the results in the standard output formats (Fig. 26A). Below is a table with graphical results that can be viewed by clicking the arrows to expand the section (Fig. 26B).
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Figure 26. Results from BLAST module.
Users can also view the alignments to the genome scaffolds in JBrowse using the hyperlink to the scaffold (Fig. 27A). To see the BLAST result in JBrowse, click the box in the JBrowse left-side menu (Fig. 27B). Features that are in the PCDdatabase (CDS, peptides, unigenes, RefTrans), will have links to more information in PCD.
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Figure 27. BLAST link to JBrowse.