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» A Computational Model for RNA Multiple Structural Alignment.
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BMCBI
2007
109views more  BMCBI 2007»
13 years 9 months ago
Computational RNA secondary structure design: empirical complexity and improved methods
Background: We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various cl...
Rosalía Aguirre-Hernández, Holger H....
JCB
2007
94views more  JCB 2007»
13 years 9 months ago
Locality and Gaps in RNA Comparison
Locality is an important and well-studied notion in comparative analysis of biological sequences. Similarly, taking into account affine gap penalties when calculating biological ...
Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M...
BIB
2008
86views more  BIB 2008»
13 years 9 months ago
Recent developments in the MAFFT multiple sequence alignment program
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reas...
Kazutaka Katoh, Hiroyuki Toh
BMCBI
2006
95views more  BMCBI 2006»
13 years 9 months ago
A quantitative analysis of secondary RNA structure using domination based parameters on trees
Background: It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary...
Teresa W. Haynes, Debra J. Knisley, Edith Seier, Y...
BIOCOMP
2006
13 years 10 months ago
PAC: Progressive Alignment with Consensus Sequences
Computation of multiple sequence alignments is one of the major open problems in computational molecular biology. The purpose of this study was to provide a new method, PAC (Progre...
Ke Liu, Mansur H. Samadzadeh