AI Article Synopsis
- ExtraTrain is a comprehensive database focused on transcriptional regulation in prokaryotes, featuring information on 679,816 extragenic regions and regulatory proteins from bacteria and archaea.
- The platform includes an interactive tool called Palinsight for exploring palindromic patterns in regulatory signals within user-defined extragenic regions.
- ExtraTrain aims to be a community-driven resource, allowing researchers to contribute knowledge and maintain an extensive, curated repository of transcriptional regulation data, accessible at http://www.era7.com/ExtraTrain/.
Article Abstract
Background: Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory DNA signals located in extragenic regions are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the UniProt database.
Description: ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. In addition 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 belong to the families AraC/XylS, ArsR, AsnC, Cold shock domain, CRP-FNR, DeoR, GntR, IclR, LacI, LuxR, LysR, MarR, MerR, NtrC/Fis, OmpR and TetR. The database follows the InterPro criteria to define these families. 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.
Conclusion: ExtraTrain is a new database for exploring Extragenic regions and Transcriptional information in bacteria and archaea. ExtraTrain database is available at http://www.era7.com/ExtraTrain/.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1453763 | PMC |
| http://dx.doi.org/10.1186/1471-2180-6-29 | DOI Listing |
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