Results 31 to 40 of about 1,311,103 (281)
Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing [PDF]
, 2003 Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological
Gilbert, D, Westhead, DR, Williams, A
core +1 more source
Optimization of sequence alignment for simple sequence repeat regions
BMC Research Notes, 2011 Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome.
Ogbonnaya Francis C +2 more
doaj +1 more source
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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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
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Sequence Alignment as Hypothesis Testing [PDF]
Journal of Computational Biology, 2011 Sequence alignment depends on the scoring function that defines similarity between pairs of letters. For local alignment, the computational algorithm searches for the most similar segments in the sequences according to the scoring function. The choice of this scoring function is important for correctly detecting segments of interest.
Lu Meng +3 more
openaire +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
doaj +1 more source
NovoLign: metaproteomics by sequence alignment. [PDF]
ISME CommunABSTRACT Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome ...
Kleikamp HBC +8 more
europepmc +4 more sources
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
BMC Bioinformatics, 2010 Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám +3 more
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Fair Evaluation of Global Network Aligners [PDF]
, 2014 Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different ...
Crawford, Joseph +2 more
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