Results 31 to 40 of about 483,132 (293)

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, Otu Hasan H, Russell David J   +2 more
doaj   +1 more source

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

GLProbs [PDF]

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, 2013
This paper introduces a simple and effective approach to improve the accuracy of multiple sequence alignment. We use a natural measure to estimate the similarity of the input sequences, and based on this measure, we align the input sequences differently.
Yongtao Ye, David W. Cheung, Yadong Wang 0001, Siu-Ming Yiu, Qing Zhan, Tak Wah Lam, Hing-Fung Ting   +6 more
openaire   +5 more sources

Multiple sequence alignment with the Divide-and-Conquer method.

, 1998
Stoye J. Multiple sequence alignment with the Divide-and-Conquer method. Gene. 1998;211(2):GC45-GC56.An improved algorithm for the simultaneous alignment of multiple protein and nucleic acid sequences, the Divide-and-Conquer Alignment procedure (DCA), is
Jens Stoye, Stoye, Jens ; https://orcid.org/   +1 more
core   +1 more source

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.
Sırrı Yüzbaşıoğlu, Taşçı Nivart, O Uğur Sezerman, Bakis, Yasin, Yuzbasioglu, Sirri, Neş’e Bilgin, Sezerman O Uğur, Cem Meydan, Yasin Bakış, Bakış Yasin, Sezerman, Uğur, Taşçı, Nivart, Bilgin, Nes'e, Bilgin, Neşe, Yüzbaşıoğlu, Sırrı, Meydan Cem, Bakış, Yasin, Otu Hasan H, Sezerman, O. Ugur, Meydan, Cem, Yüzbaşıoğlu Sırrı, Otu, Hasan H., Hasan H Otu, Nivart Taşçı, Tasci, Nivart, Bilgin Neş’e   +25 more
core   +1 more source

Scaling statistical multiple sequence alignment to large datasets

BMC Genomics, 2016
Background Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest.
Michael Nute, Tandy Warnow
doaj   +1 more source

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Viruses, 2022
The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data.
Colin Young, Sarah Meng, Niema Moshiri
doaj   +1 more source

An iterative method for faster sum-of-pairs multiple sequence alignment

, 2000
Reinert K, Stoye J, Will T. An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics.
Stoye, Jens ; https://orcid.org/, Reinert, Knut, Will, Torsten   +2 more
core   +1 more source

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

BMC Bioinformatics, 2011
Background Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif ...
Deng Xin, Cheng Jianlin
doaj   +1 more source

Divide-and-conquer multiple alignment with segment-based constraints

, 2003
Sammeth M, Morgenstern B, Stoye J. Divide-and-conquer multiple alignment with segment-based constraints. BIOINFORMATICS. 2003;19(Suppl 2):ii189-ii195.A large number of methods for multiple sequence alignment are currenty available.
Sammeth, Michael, Stoye, Jens ; https://orcid.org/, Morgenstern, Burkhard   +2 more
core   +1 more source