Results 31 to 40 of about 1,276,854 (326)
Accelerated large-scale multiple sequence alignment
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of ...
Lloyd Scott, Snell Quinn O
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Using structure to explore the sequence alignment space of remote homologs. [PDF]
PLoS Computational Biology, 2011 Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate ...
Andrew Kuziemko +2 more
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Strategies for Multiple Sequence Alignment
BioTechniques, 2002 We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence ...
Hugh B. Nicholas +2 more
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Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450 [PDF]
, 2006 Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection.
Arnold, Frances H. +5 more
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BEAST: Bayesian evolutionary analysis by sampling trees [PDF]
, 2007 Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics ...
Drummond, Alexei J., Rambaut, Andrew
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Multiple sequence alignment accuracy and evolutionary distance estimation
BMC Bioinformatics, 2005 Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and ...
Rosenberg Michael S
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Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure [PDF]
, 2013 Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees.
Bakis, Yasin +11 more
core +2 more sources
PLoS ONE, 2020 Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural ...
Amir H Bayegan, Peter Clote
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A Mutual Information Based Sequence Distance For Vertebrate Phylogeny Using Complete Mitochondrial Genomes [PDF]
, 2007 Traditional sequence distances require alignment. A new mutual information based sequence distance without alignment is defined in this paper. This distance is based on compositional vectors of DNA sequences or protein sequences from complete genomes ...
Anh, Vo +3 more
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Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment
, 2019 Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures.
Alkan, Can +4 more
core +2 more sources