1D – DNA and RNA sequences manipulation:

Sequence editor  

DNA primers design (for PCR)

2D – RNA and DNA folding software:

Two state hybridization server

UNAfold

NUPACK

3D – Nucleic Acid modeling and structure prediction programs:

PyMOL 

SwissPDB viewer

Vfold

Databases:

Nucleic Acid Database (NDB)

Protein data bank (PDB)