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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Spark-based Parallelization of Basic Local Alignment Search Tool [PDF]
International Journal Bioautomation, 2020 Sequence alignment is a key link of bioinformatics analysis. The basic local alignment search tool (BLAST) is a popular sequence alignment algorithm with high accuracy. However, the BLAST is inefficient in comparing and analyzing a massive amount of gene
Hui Wang +4 more
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Sequence‐to‐sequence alignment using a pendulum
IET Computer Vision, 2015 Analysing two or more video sequences of dynamic scenes typically requires time synchronisation between sequences, where this alignment is not always possible using hardware.
Tomislav Pribanic +2 more
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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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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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Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences
IEEE Access, 2019 The computational techniques for nucleic acid and protein sequence comparison reduce the extensive burden of molecular biologists. The sequence alignment is one of the main research areas in bioinformatics, and comparative genomics and proteomics lead us
Muhammad Ishaq +3 more
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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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ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
PLoS Biology, 2020 Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference.
J. Steenwyk +4 more
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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
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity
BMC Bioinformatics, 2004 BackgroundIn a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy
Robert C. Edgar
semanticscholar +1 more source