RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

Background: With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results: RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA stru...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, Xiuzi Ye
• Keywords: BMCBI 2008, Informational Complexity, Rna Sequences, Secondary Structure