A user guide for the SorghumBase database is available
Is it sometimes hard to know where to start? If you are an old or new user of SorghumBase resources, we recommend you review our new quick user guide for exploring the Sorghum PanGenome. The guide is available at https://www.sorghumbase.org/guides.
To support the user experience, the guide takes you on a tour of the site using the MSD2 gene, which encodes a lipoxygenase (LOX) that catalyzes the first committed step of jasmonic acid biosynthesis, as the exemplar model, using its gene identifier:
The guide demonstrates how to search for a gene in the site’s search interface and describes various views of the gene structure and associated data, such as gene family trees with color-coded protein domains, amino acid alignments across a tree, and gene neighborhood views. Other data cross-linked from collaborators are Plant Reactome pathways and EBI-Atlas gene expression. In addition, users are taken through the sorghum pangenome installation on the Ensembl browser, including gene and transcript pages, protein domains view, mRNA and protein alignments, comparative analysis data such as gene family trees, whole-genome alignments, and synteny maps, genetic and structural variation including naturally occurring SNPs and chemically -induced EMS point mutations, phenotypic variation (QTL data), gene regulation (RNA-Seq gene expression), how to add/remove custom data tracks, and relevant literature references.