The RNA World : the nature of modern RNA suggests a prebiotic RNA world by 
RNA 3D Structure Analysis and Prediction by 
In Silico RNA to Protein Translation:
Enter a DNA or RNA sequence for conversion to protein sequence in all 6 reading frames. Many codon table variants are available, including vertebrate mitochondrial, yeast mitochondrial, invertebrate mitochondrial and alternate yeast nuclear codes.
Prokaryotic Operon Prediction Databases:
Prokaryotic Operon Database (ProOpDB)
A database containing the predicted operon structures of more than 1200 prokaryotic organisms searchable by organism name, metabolic pathway (Kyoto Encyclopedia of Genes and Genomes (KEGG) database), gene orthology (Clusters of Orthologous Groups (COG) database), conserved structure (Protein Families (Pfam) database), reference gene and reference operon.
A database of predicted microbial operon structures based on the detection of gene pairs. Calculated probablilities that genes actually belong to the same operon (as opposed to genes being merely adjacent) consider proximity and order due to a common ancestor as well as the possiblility of horizontal gene transfer.
References:
Taboada B, Ciria R, Martinez-Guerrero CE, Merino E. 2012. ProOpDB: Prokaryotic Operon DataBase. Nucleic Acids Research 40(D1):D627-D631.
Taboada B, Verde C, Merino E. 2010. High accuracy operon prediction method based on STRING database scores. Nucleic acids research 38(12):e130-e130.
Ermolaeva MD, White O, Salzberg SL. 2001. Prediction of operons in microbial genomes. Nucleic acids research 29(5):1216-1221.
Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. 2009. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Research 37(suppl_1):D479-D482.
About RNA Secondary Structure Prediction Programs:
The ViennaRNA Web Services (University of Vienna)
This server provides programs, web services, and databases provided by the University of Vienna related to RNA secondary structures.
RNAstructureWeb (University of Rochester)
A collection of RNA folding prediction algorithms.
UNAfold (replaces the veteran "Mfold")
UNAfold (for "Unified Nucleic Acid Folding and hybridization package") provides predicted secondary structures for input ssRNA or ssDNA sequences as well as predicted hybridizations between pairs of single stranded nucleic acid polymers. The package also predicits UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species as a function of temperature. ITC (Isothermal Titration Calorimetry) and van 't Hoff plots are also simulated.
An RNA secondary structure predition program based on the algorithym published by Zucker and Steigler (1981). This program predicts the conserved structure from a series of aligned RNA sequences.
Note that this is very different than UNAfold, which provides predicted secondary structures for individual ssRNA or ssDNA sequences.
IPknot: IP-based prediction of RNA pseudoKNOTs
Provides services for predicting RNA secondary structures including a wide class of pseudoknots.
The ProbKnot server takes a sequence file of nucleic acids, either DNA or RNA, and predicts the presence of pseudoknots in its folded configuration.
References:
Zuker M, Stiegler P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic acids research 9(1):133-148.