ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
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.


METHODS
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.


CONCLUSIONS
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/.
Pareja
Eduardo
E
Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud, Armilla Granada 18100, Spain. epareja@era7.com
Pareja-Tobes
Pablo
P
Manrique
Marina
M
Pareja-Tobes
Eduardo
E
Bonal
Javier
J
Tobes
Raquel
R
D001105:Archaea / Q000235:genetics*; D019843:Archaeal Proteins / Q000378:metabolism; D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D030541:Databases, Genetic; D023281:Genomics; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D016415:Sequence Alignment; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D014157:Transcription Factors