: FASH (Fourier Alignment Sequence Heuristics) is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a ...
Isana Veksler-Lublinsky, Danny Barash, Chai Avisar...
INFO-RNA is a new web server for designing RNA sequences that fold into a user given secondary structure. Furthermore, constraints on the sequence can be specified, e.g. one can r...
Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of ne...
Background: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel ...
Background: Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for tak...
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 neede...
Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, ...
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structu...
Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of...
In this paper, we consider the pattern matching problem in DNA and RNA sequences where either the pattern or the text can be degenerate i.e. contain sets of characters. We present ...
M. Sohel Rahman, Costas S. Iliopoulos, Laurent Mou...
We are building a knowledge base (KB) of published structural data on the 30s ribosomal subunit in prokaryotes. Our KB is distinguished by a standardized representation of biologi...
Russ B. Altman, Neil F. Abernethy, Richard O. Chen