This section contains help guides on how to use the features in the TRNDiff online web application.
Before you can see any view, you will need to load some data. The online application is connected directly to the RegPrecise database.
RegPrecise is a repository of high-quality reference data which captures the regulatory relationships between genes in 390 prokaryote genomes. The database contains manually curated details of genes, transcription factors and transcription factor binding sites which have been obtained by careful comparative genomic analysis, experimentation and literature review as outlined in the paper:
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 January; 38(Database issue): D111–D118.
TRNDiff is intended to provide an easy way to browse the RegPrecise database, locate a regulog of interest, and view the regulons belonging to the regulog. Any regulog can be saved to the desktop in CSV format, and these files can be edited and then reloaded into the program to view the results.
Future versions of this application will provide further integration of TRNDiff and RegPrecise with standard tools such as NCBI BLAST to allow users to execute more powerful workflows.