Abstract：Resources on the Internet of RNA were reviewed by Chen et al. in 2000. However, since 2000, a remarkable progress has been made on research of RNA. Non-coding RNA (ncRNA)，which is not translated into a protein，becomes one of the hottest topics in modern molecular biology. We summarized that new progress on internet resources of sequence, structure, web tool and software related to non-coding RNA from 2000 to end of May, 2007. 1) We found over 50 sequence databases of ncRNA on the Internet. About 30 million sequences were collected in those databases. Integrated databases, e.g. NONCODE and RNAdb, mainly provide original sequence information of various types of non-coding ncRNA. Specialized databases, such as miBase, miRNAMAP and HuSiDa, offer not only sequences but functions, structure, reference etc. of a certain type of ncRNA. 2) We searched 13 structure databases of ncRNA and about 1,200 crystal structures and hundreds of forecasted structures. NDB and PDB supply information on crystal structure of ncRNA measured by NMR spectroscopy and by X-ray crystallography. Rfam and CRW contain secondary structure of ncRNA predicted by comparative sequence analysis. SCOR, RAG and MeRNA offer specialized information such as structure classification, topological structure, and special structure. 3) About 30 software tools were available on the Internet for ncRNA analysis. Mfold was developed to predict secondary structure of RNA. miRanda, TargetScan, PictTar and RNAhybrid are used for predicting miRNA’s target gene. Amibion, Invivoge and Whitehead offer the function of siRNA design. PHYLIP, MEGA, PAUP* are famous software for analysis of phylogenetics. In addition, we discussed the bioinformatic works we need do in near future, i.e. to develop 1) a search engine of ncRNA, 2) a new approach for predicting secondary structure of ncRNA, and 3) a method to mine the potential information of sequence and structure of ncRNA.
