The Biofuel Feedstock Genomics Resource (BFGR) is a USDA/DOE funded project that provides annotation for gene and transcript sequences from lignocellulosic biofuel feedstock species. Except for the few plant species that have fully sequenced genomes, annotation of these sequence resources can be lacking, and when present, the annotation quality can vary greatly. For many plant species that are being used for lignocellulosic biofuel feedstock research, there is limited genomic and transcript sequence data. BFGR provides uniform annotation for all gene and transcript sequence data that is available for lignocellulosic biofuel feedstock species, and sequences from different species can be easily related to each other to allow researchers to leverage data between species.
For those biofuel feedstock species without fully sequenced genomes, transcript assemblies serve as surrogate gene sequences within BFGR, and those sequences have been analyzed and annotated. We use PUT transcript assemblies from PlantGDB for the analyses performed here. Additionally, the gene and protein sequences from Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Sorghum bicolor and Vitis vinifera have been similarly analyzed.
Analyses of the gene and transcript sequences within BFGR include blast alignments to the gene sets of Oryza sativa, Arabidopsis thaliana, Populus trichocarpa, Sorghum bicolor and Vitis vinifera. All sequences have also been aligned to UniRef proteins and to Pfam protein families and domains. Functional annotations have been assigned based on alignments to UniRef and Pfam sequences. SSRs have been identified in all PUT-based sequences in order to help researchers identify possible genetic polymorphisms. Search pages allow researches to identify various types of SSRs. Researchers can also perform BLAST-based searches against the gene, protein and PUT transcript sequences within BFGR. Text-based searching against functional annotation terms is also available. All gene and transcript sequences link to individual Annotation Report Pages that provide a unified view of all of the annotation that is available for each sequence.