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Bioinformatics is of paramount importance for protein analysis in proteomic and transcriptomic studies. Proteomics and transcriptomics generate huge amounts of data that must be interpreted to answer biological questions. Bioinformatics is used at two steps of proteomic studies: (i) identification of proteins by peptide mass mapping or peptide sequencing and, (ii) analysis of protein sequences to predict their sub-cellular localization, their function and eventually sites of post-translational modifications. It is also used to sort genes identified by transcriptomic studies in functional classes. In addition, bioinformatics can provide predictions of co-expression networks thus allowing to visualize biological networks.
To facilitate interpretation of proteomic and transcriptomic data, ProtAnnDB (Protein Annotation DataBase) collects predictions of sub-cellular localization and of functional domains made by available software and provides scores to assess the quality of these predictions. When available, expert annotations have been indicated, e.g. links to the redoxibase for the class III peroxidases. It also provides Planet predictions, which allow looking for gene co-expression networks in several plants.
In its last version, ProtAnnDB is devoted to protein sequences of:
| Dicots | Monocots | Bryophytes |
|---|---|---|
|
Arabidopsis thaliana Arabidopsis lyrata Beta vulgaris Brassica oleracea var. capitata Eucalyptus grandis Fagopyrum esculentum Fagopyrum tataricum Glycine max Gossypium raimondii Helianthus annuus Linum usitatissimum Malus domestica Medicago truncatula Populus trichocarpa Solanum lycopersicum Solanum tuberosum Theobroma cacao |
Brachypodium distachyon Oryza sativa Sorghum bicolor Triticum aestivum Zea mays |
Marchantia polymorpha Physcomitrella patens |
ProtAnnDB is regularly completed with sequences from other plants.
The authors wish to thank the Plateforme de Bioinformatique GenoToul Midi-Pyrénées in Toulouse (France) for providing calculation facilities for the rice sequences (bioinfo.genotoul.fr).
If you use ProtAnnDB, please cite:
Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: Plant cell wall proteomics as a test case
H San Clemente, R Pont-Lezica and E Jamet
Bioinform Biol Insights 3:15-28, 2009.
Contact: Elisabeth JAMET (elisabeth.jamet@univ-tlse3.fr)
Webmaster: Hélène San Clemente (helene.san-clemente@univ-tlse3.fr)
Last update: September 25th 2023
