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SCFBM
2008
131views more  SCFBM 2008»
13 years 10 months ago
FASH: A web application for nucleotides sequence search
: 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...
NAR
2007
106views more  NAR 2007»
13 years 10 months ago
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints
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...
Anke Busch, Rolf Backofen
JCB
2002
111views more  JCB 2002»
13 years 10 months ago
A General Edit Distance between RNA Structures
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...
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
BMCBI
2008
145views more  BMCBI 2008»
13 years 11 months ago
Directed acyclic graph kernels for structural RNA analysis
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 ...
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubum...
BMCBI
2008
83views more  BMCBI 2008»
13 years 11 months ago
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
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...
Akito Taneda
BMCBI
2008
117views more  BMCBI 2008»
13 years 11 months ago
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 neede...
Qi Liu, Yu Yang, Chun Chen, Jiajun Bu, Yin Zhang, ...
BIOSYSTEMS
2007
104views more  BIOSYSTEMS 2007»
13 years 11 months ago
New structural variation in evolutionary searches of RNA neutral networks
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structu...
Sumedha, Olivier C. Martin, Andreas Wagner
BMCBI
2010
139views more  BMCBI 2010»
13 years 11 months ago
RNAstructure: software for RNA secondary structure prediction and analysis
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...
Jessica S. Reuter, David H. Mathews
WALCOM
2007
IEEE
109views Algorithms» more  WALCOM 2007»
14 years 1 days ago
Pattern Matching in Degenerate DNA/RNA Sequences
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...
ISMB
1997
14 years 7 days ago
Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data
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