UMass Amherst


Softwares and Servers

  • NUPACK: analysis and design of nucleic acid structures
  • mFold & UNAFold: nucleic acid folding and hybridization prediction
  • LocARNA: RNA alignment and folding
  • OligoCalc: DNA/RNA properties calculator
  • KineFold: animating RNA folding
  • caDNAno: DNA origami design program
  • CanDo: predicting 3D shape and flexibility of programmed DNA assembly
  • DAEDALUS: DNA origami sequence design algorithm for user-defined structures
  • NanoTiler: design of RNA nanostructure
  • RNA2D3D: convert RNA 2D structures to 3D modeling
  • SnapGene: plasmid map editor
  • ApE: another plasmid map editor
  • EteRNA: a browser-based game to solve puzzles about RNA folding
  • sciNote: free open source electronic lab notebook

Database and Protocols

  • Nucleic Acid Database: experimentally-determined 3D nucleic acids and complex assemblies
  • RNAJunction: database for RNA junction and kissing loop
  • Rfam: RNA families database
  • Bionumbers: database of useful biological numbers
  • Benchfly: science video platform with many useful protocols and techniqeus
  • JoVE: Journal of Visualized Experiments, with movies for many detailed protocols and techniques
  • Protocol Online: protocols and forum discussion
  • NEB Tools & Resources: New England Biolabs