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ExtraTrain


NAR Molecular Biology Database Collection entry number 913
Tobes, R., Pareja, E., Pareja-Tobes, P., Manrique, M., Pareja-Tobes, E. Bonal, J.
Bioinformatics Unit, Era7 Information Technologies, C Río Tajo 49. Granada 18110, Spain
Contact rtobes@era7.com

Database Description

ExtraTrain is a new database for exploring Extragenic and Transcriptional information in prokaryotic organisms. Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory signals located in DNA extragenic regions and the regulatory proteins are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and all regulatory proteins included in the UniProt database corresponding to bacteria and archaea. ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. ExtraTrain supplies a tool to explore extragenic regions, named Palinsight, oriented to detect and search palindromic patterns. This interactive visual tool is totally integrated in the database, allowing the search for regulatory signals in user defined sets of extragenic regions. The 26046 regulatory proteins included in ExtraTrain are classified in 16 families following the InterPro criteria. The information about regulators includes manually curated sets of references specifically associated to regulator entries. In order to achieve a sustainable and maintainable knowledge database ExtraTrain is a platform open to the contribution of knowledge by the scientific community providing a system for the incorporation of textual knowledge by the scientists. ExtraTrain database is available at http://www.era7.com/ExtraTrain/.

Acknowledgements

This work has been financed by Era7 Information Technologies SL.


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