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WABI
2005
Springer
120views Bioinformatics» more  WABI 2005»
14 years 3 months ago
Multiple Structural RNA Alignment with Lagrangian Relaxation
In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence ...
Markus Bauer, Gunnar W. Klau, Knut Reinert
BIOCOMP
2007
13 years 11 months ago
Quality-Based Similarity Search for Biological Sequence Databases
Low-Complexity Regions (LCRs) of biological sequences are the main source of false positives in similarity searches for biological sequence databases. We consider the problem of ï...
Xuehui Li, Tamer Kahveci
BMCBI
2006
117views more  BMCBI 2006»
13 years 10 months ago
Incorporating background frequency improves entropy-based residue conservation measures
Background: Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may corr...
Kai Wang, Ram Samudrala
GCB
2004
Springer
139views Biometrics» more  GCB 2004»
14 years 3 months ago
Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites
: We introduce the novel concept of graph alignment, a generalization of graph isomorphism that is motivated by the commonly used multiple sequence alignments. Graph alignments and...
Nils Weskamp, Eyke Hüllermeier, Daniel Kuhn, ...
ALMOB
2008
81views more  ALMOB 2008»
13 years 10 months ago
Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
Background: Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments....
Holger Wagner, Burkhard Morgenstern, Andreas W. M....