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» Multiple RNA Structure Alignment
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BMCBI
2011
13 years 4 months ago
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Background: The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state...
Zsuzsanna Sukosd, Bjarne Knudsen, Morten Vaerum, J...
BMCBI
2006
158views more  BMCBI 2006»
13 years 10 months ago
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
Background: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical s...
Andrew V. Uzilov, Joshua M. Keegan, David H. Mathe...
BIOINFORMATICS
2006
111views more  BIOINFORMATICS 2006»
13 years 10 months ago
Multiple Alignment of protein structures and sequences for VMD
Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the ali...
John Eargle, Dan Wright, Zaida Luthey-Schulten
CPM
2006
Springer
112views Combinatorics» more  CPM 2006»
14 years 1 months ago
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes
Abstract. Local similarity is an important tool in comparative analysis of biological sequences, and is therefore well studied. In particular, the Smith-Waterman technique and its ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
NAR
2006
128views more  NAR 2006»
13 years 9 months ago
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify cl...
Fabrice Armougom, Sébastien Moretti, Olivie...