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» Multiple RNA Structure Alignment
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RECOMB
2009
Springer
14 years 10 months ago
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted seconda...
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
BMCBI
2006
139views more  BMCBI 2006»
13 years 10 months ago
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise li
Background: Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy...
Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
BMCBI
2005
119views more  BMCBI 2005»
13 years 9 months ago
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Background: We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a q...
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
BMCBI
2006
108views more  BMCBI 2006»
13 years 10 months ago
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Background: Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. How...
Hanno Teeling, Frank Oliver Glöckner
AINA
2006
IEEE
14 years 3 months ago
Partitioned optimization algorithms for multiple sequence alignment
Multiple sequence alignment is an important and difficult problem in molecular biology and bioinformatics. In this paper, we propose a partitioning approach that significantly impr...
Yixin Chen, Yi Pan, Juan Chen, Wei Liu, Ling Chen