Data sources
Genome sequences
| Organism | Source and release | Number of sequences |
| Oryza sativa | v6 | 67393 |
| Arabidopsis thaliana | v9 | 33200 |
| Medicago truncatula | v2 | 38749 |
| Sorghum bicolor | v1.4 | 36338 |
| Populus trichocarpa | v1.1 | 45555 |
| Vitis vinifera | v1 | 30434 |
| Physcomitrella patens | v1.1 | 35938 |
| Selaginella moellendorffii | v1 | 34697 |
| Glycine max | v1 | 75778 |
| Ostreococcus tauri | v2 | 7725 |
| Chlamydomonas reinhardtii | v4 | 16706 |
| Cyanidioschyzon merolae | v1 | 5014 |
| Brachypodium distachyon | v1 | 44411 |
| Carica papaya | n/a | 24782 |
| Ricinus communis | v0.1 | 31221 |
| Zea mays | v4 | 53764 |
Remark about sequence identifiers
Sequences are usually identifed by a the locus tags defined by the consortia responsible of the annotation (e.g. At5g20240.1). For some draft genomes, we have modified id using scaffold id_ species code (e.g. Phypa_96903)
Data associated to genomes
Protein domain and domain architecture
Each sequences was analysed using InterProScan to identify InterPro domain [1](InterPro 16.2, 04 February 2008)Each group of sequence was analysed using Meme/Mast to define domain his domain architecture. [2, 3]
UniProt (Universal Protein Resource)
Correspondance between UniProtKB [4]( last update: 22 may 2009) was made on the ordered locus when available (in 'Gene names' section).
Otherwise, mapping was done using the first blast hit of blast having anidentity score > 90%.
Uniprot Taxonomy
Kegg (Kyoto Encyclopedia of Genes and Genomes)
Kegg [5] data were download from the KEGG Orthology (KO) Database when available (last update: 02/02/2009)
Gene Ontology (Controlled vocabulary of terms for describing gene product)
GO terms, and particularly Plant GOslim, were obtained from the interpro and UniProt.
Pubmed
Clusters are tag by selected pubmed id referenced in UniProt entries. Annotator can also add their own publications.
References
- Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.
- Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
- Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, Vol. 14, pp. 48-54, 1998.
- Schneider M, Bairoch A, Wu CH, Apweiler R. Plant protein annotation in the UniProt Knowledgebase.Plant Physiol. (2005) 138:59-66
- Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
