Future Plans
Future releases of the Biofuel Feedstock Genomics Resource (BFGR) will contain additional sequence data, new analyses and additional tools for researchers.
- As new plant genomic sequences become publicly available, they will be added to BFGR. All transcript assembly and gene sequences within BFGR will be annotated relative to the newly available gene models and genome.
- In the next major release of BFGR, newly updated PUT transcript assembly collections for any BFGR species will be incorporated into the BFGR pipeline, annotated and added to our database.
- If new PUT transcript assembly collections become available for species that are of interest to lignocellulosic biofuels research but that are not currently included in BFGR, those species and their PUT sequences will be added to this resource. If your biofuel feedstock species is not part of BFGR but should be, please contact us.
- Open reading frame analysis will be performed on all PUT transcript assembly sequences within BFGR and predicted protein translations will be made available through each PUT's Annotation Report Page.
- Analyses will be performed on the gene and transcript sequences within BFGR to determine paralogous and orthologous sequence groups. This will allow researchers to more easily traverse between species that do not have fully sequenced genomes.
- Rice has a large quantity of publicly available expression data. Those data will be used to infer gene associations and gene networks in rice. Sequences from individual species within BFGR will be overlayed on the rice gene networks to allow researchers to hypothesize about gene networks in other species.
- All sequences will be hyperlinked to other public resources in which large-scale functional genomic data is housed. Links will be added to the Annotation Report Pages to relavent data from databases such as the NCBI Gene Expression Omnibus (GEO), PlexDB, the Massively Parallel Signature Database and the PlantsP (Plant Phosphorylation) database.
- Using meta-data that is associated with EST sequences from dbEST, we will create an electronic Northern tool for all gene and transcript sequences in BFGR. This will be similar to the electronic Northern tool that is currently available at the MSU Rice Genome Annotation Project.
- Additional functional annotation will be assigned after performing analyses with a subset of the InterPro suite of protein family, domain and site databases. These databases will included PROSITE, PRINTS, ProDom, UniProt, SMART and PANTHER.
- Gene Ontology terms will be assigned to sequences and added to the Annotation Report Pages. Text-based searching will be expanded to include these GO terms.
- Gene and transcript sequences within BFGR will be mapped to the KEGG biochemical pathways. Researchers will be able to view all sequences from a given species that map to a specific KEGG pathway. Pathway membership, E.C. numbers, presumptive enzyme names and links to graphical pathway maps will be added to the Annotation Report Pages.
- The databases that are searchable by BLAST will be expanded to include pseudomolecule sequences from the fully sequenced plant genomes. The results from BLAST alignments will be linked to the BFGR genome browsers.
- Text-based searches are currently limited. Text-based searching will be made more powerful.