Results 31 to 40 of about 756,544 (331)
Protein Multiple Sequence Alignment [PDF]
, 2008 Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy or scalability of multiple and pairwise ...
Chuong B, Do, Kazutaka, Katoh
openaire +2 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
doaj +1 more source
Lower bounds on multiple sequence alignment using exact 3-way alignment
BMC Bioinformatics, 2007 Background Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently
Colbourn Charles J, Kumar Sudhir
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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
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
BMC Bioinformatics, 2003 Background The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of ...
Searle Stephen MJ +4 more
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MAFFT version 5: improvement in accuracy of multiple sequence alignment
Nucleic Acids Research, 2005 The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective ...
K. Katoh, K. Kuma, H. Toh, T. Miyata
semanticscholar +1 more source
Developments in Algorithms for Sequence Alignment: A Review
Biomolecules, 2022 The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately.
Jiannan Chao, Furong Tang, Lei Xu
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SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Bioinform., 2012 MOTIVATION In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly
E. Pruesse, J. Peplies, F. Glöckner
semanticscholar +1 more source
Grammar-based distance in progressive multiple sequence alignment
BMC Bioinformatics, 2008 Background We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms.
Sayood Khalid +2 more
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ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes
bioRxiv, 2020 Motivation In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data.
Niema Moshiri
semanticscholar +1 more source