What's New
17 July 2009
Release 2.2 of the Biofuel Feedstock Genomics Resource is available.
- Predicted peptide sequences for PlantGDB PUT-based sequences have been added to the annotation report pages. These sequences were predicted using ESTScan. See the FAQ page for discussion about ESTScan protein sequence predictions with the PUTs.
- Links to Germplasm Resources have been added to the Species Overview pages.
- The BLAST search form has been moved to the unified search page.
- Improvements to the database should cause the Annotation Report Page to load more quickly.
- A Quick Annotation Search form has been added to the BFGR home page.
11 May 2009
Release 2.1 of the Biofuel Feedstock Genomics Resource is available.
- Computationally identified SNPs have been identified and are viewable within the annotation report pages.
- The various search pages have been combined into a single unified search page which includes a form for identifying sequences with SNPs.
- The results of SSR and SNP searches can be returned as either HTML or tab-delimited text. There is also the option to return tab-delimited text results with the functional annotations of the sequences.
- A new page that describes our future plans has been added to the website.
- A FAQ page is also available with answers to questions that a typical user may have.
10 April 2009
Release 2 of the Biofuel Feedstock Genomics Resource is available.
- The Sorghum bicolor genome has been added to the BFGR database. A sorghum-based genome browser has been added to the existing browsers. All of the transcript assemblies (PlantGDB PUTs) from 18 species used for biofuel feedstock research have been aligned to the Sorghum bicolor genome. The transcripts from the other four model genomes (Oyrza sativa, Populus trichocarpa, Arabidopsis thaliaha and Vitis vinifera) have been aligned to this genome. Best hits between Sorghum bicolor proteins and the proteomes from each of Oyrza sativa, Populus trichocarpa, Arabidopsis thaliana and Vitis vinifera are also displayed in the browser.
- The Sorghum bicolor gene set is now used in place of the Sorghum bicolor transcript assemblies. The transcripts from these gene sequences have been aligned to the genomes of Oyrza sativa, Populus trichocarpa, Arabidopsis thaliaha and Vitis vinifera and are displayed in the browsers for those species. The Sorghum bicolor protein sequences have been aligned to the protein sequences from the other model genomes and best hits between the proteomes are also displayed in the browsers.
- Functional annotation has been assigned to all sequences except those from Oryza sativa and Arabidopsis thaliana, which have their own official functional annotations. All BFGR sequences were aligned by BLAST to a special set of UniRef sequences that contains all UniRef50 sequences and those UniRef100 sequences that were derived from Embryophyta (higher plant) species. All BFGR sequences were also aligned by RPSBLAST to Pfam protein families and domains. Functional annotations for BFGR sequences were taken from the best possible UniRef sequence hit, but if that was not possible, functional annotations were made based on the best Pfam domain alignment. If the available functional annotation was not useable, PUT-based sequences were given a functional annotation of "Conserved expressed gene of unknown function". If there were no hits to UniRef or Pfam sequences, PUT-based sequences were given a functional annotation of "Expressed gene of unknown function". For Sorghum bicolor, Populus trichocarpa and Vitis vinifera, the analogous terms were "Conserved gene of unknown function" and "Gene of unknown function".
- SSRs have been identified in all PUT transcript assembly sequences. Information about SSRs are displayed in the Annotation Report page for each sequence. Additionally, an SSR search tool is available that allows researchers to find various classes of SSRs from particular species. Primer sequences that can be used to amplify SSRs have also been perdetermined when possible.
- An annotation search tool is now available for searching the functional annotation descriptions of a single species or all species.
- A sequence id search tool is also available to find the Annotation Report page for a particular sequence.
8 February 2009
Release 1 of the Biofuel Feedstock Genomics Resource is available.
- Transcript assemblies (PlantGDB PUTs) from 19 species used for biofuel feedstock research have been filtered, annotated and aligned to the genomes of Oyrza sativa, Populus trichocarpa, Arabidopsis thaliaha and Vitis vinifera. The biofuel feedstock species included in these analyses are Brachypodium distachyon, Cenchrus ciliaris, Helianthus annuus, Hordeum vulgare, Leymus cinereus x Leymus triticoides, Medicago sativa, Medicago truncatula, Panicum virgatum, Picea glauca, Picea sitchensis, Pinus taeda, Populus tremula x Populus tremuloides, Secale cereale, Sorghum bicolor, Sorghum propinquum, Triticum aestivum, Triticum turgidum subsp. durum, Triticum monococcum and Zea mays.
- The PUT sequences that have been analyzed were are a subset of those that are available from the PlantGDB. The original PlantGDB PUT sets were filtered to exclude those PUTs that are less than 250 bp in length and those that contain more than 10 ambiguous bases (a sign of poor sequence quality). The filtered PUT sets that have been analyzed are available from our FTP site.
- The genes from the official gene sets from four plant species with sequenced genomes, Oryza sativa, Populus trichocarpa, Arabidopsis thaliana and Vitis vinifera, have been analyzed and annotated in the same manner as the PUT sequences.
- Gene Report Pages can be accessed for every PUT and gene sequence that has been annotated. The Gene Report Pages contain a detailed annotation for each PUT and gene sequence.
- A genome browser has been created for the Oryza sativa, Populus trichocarpa, Arabidopsis thaliana and Vitis vinifera genomes. The genes from the sequenced genomes as well as the PUT sequences from the biofuel feedstock species have been aligned to the genome sequences and are displayed within the browsers.
- Each of the species with sequences that have been analyzed in the Biofuel Feedstock Genomics Resource has a Species Overview page that contains information about available sequence and publication resources for that species. Additional links to other web resources can also be found on the Species Overview pages.
- Genbank sequence entries and PubMed citations are followed for an additional four biofuel feedstock species PUT transcript assemblies were not available at the time that this release was being prepared. Information for these species can be found on their Species Overview pages. These species were Eleusine coracana, Miscanthus x giganteus, Pennisetum glaucum and Sorghum halepense.
- The genes that have been identified from the Sorghum bicolor genome sequencing project will be annotated in the next release of the Biofuel Feedstock Genomics Resource. At that time, the Sorghum bicolor PUTs will no longer be analyzed. Additionally, the Sorghum bicolor genome will be added to the genome browsers.