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The WebGeSTer program scans for palindromic sequence downstream of coding sequences in whole genomes. (1,2) The stability of each secondary structure is calculated using the parameters of Mathews et. al. (3). All structures identified are subjected to species-specific ΔG cut-off. All structures are classified based on the nature of their A/U-trail and the presence of adjacent structures.

      (1). Conserved economics of transcription termination in eubacteria

      Shyam Unniraman, Ranjana Prakash and Valakunja Nagaraja
      Nucleic Acid Research, 2002, Vol. 30, No. 3   675-684

      (2). Alternate Paradigm for Intrinsic Transcription Termination in Eubacteria

      Shyam Unniraman, Ranjana Prakash and Valakunja Nagaraja
      J. Biol. Chem., 2001, Vol. 276, No. 45,   42850-41855

      (3). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

      Mathews DH, Sabina J, Zuker M, Turner DH.
      J. Mol. Biol., 1999, Vol. 288, No. 5,   911-940

 Submission details 
The users have the choice to upload genome sequences in FASTA or GenBank format. The parameters are set to default. However, the user has the option to change all of them, including ΔG cut-off. The output is generated in the form of table, structures and graphs. In addition, the raw data can be downloaded manually. To incorporate your predictions into the database, please contact the authors.


                                                                       Last updated: August 15, 2010