Results 31 to 40 of about 1,008,958 (324)

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
doaj   +1 more source

Alvira : comparative genomics of viral strains [PDF]

, 2007
The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large ...
Brodie, Chenna, E. Baranowski, Edgar, F. Enault, Ghedin, Lassmann, Lee, R. Fremez, T. Faraut, Zmasek   +10 more
core   +2 more sources

Multiple sequence alignment with user-defined anchor points

Algorithms for Molecular Biology, 2006
Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.
Pöhler Dirk, Prohaska Sonja J, Morgenstern Burkhard, Stadler Peter F   +3 more
doaj   +1 more source

Aligning Multiple Sequences with Genetic Algorithm [PDF]

, 2009
The alignment of biological sequences is a crucial tool in molecular biology and genome analysis. It helps to build a phylogenetic tree of related DNA sequences and also to predict the function and structure of unknown protein sequences by aligning ...
Adebiyi, E. F., Akinyemi, I. O., Fatumo, S.   +2 more
core   +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, Otu Hasan H, Russell David J   +2 more
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

A multiple sequence alignment program

Nucleic Acids Research, 1986
A program is described for simultaneously aligning two or more molecular sequences which is based on first finding common segments above a specified length and then piecing these together to maximize an alignment scoring function. Optimal as well as near-optimal alignments are found, and there is also provided a means for randomizing the given ...
E, Sobel, H M, Martinez
openaire   +3 more sources

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

Multiple sequence alignment based on set covers

, 2004
We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the ...
A. Bahr, B. Manthey, B. Morgenstern, B. Morgenstern, C. Notredame, D. Gusfield, G. Vogt, J.D. Thompson, K. Katoh, O. Gotoh, P. Zhao, R.E. Green, R.F. Smith, S. Henikoff, T. Müller, T.P. Li   +15 more
core   +2 more sources

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment [PDF]

, 2012
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in ...
A Löytynoja, A Löytynoja, B Sipos, BG Hall, BG Hall, BP Blackburne, C Chothia, C Dessimoz, C Kemena, C Kemena, C Notredame, CB Do, CL Strope, DA Dalquen, DA Morrison, DH Mathews, ER Mardis, G Blackshields, G Jordan, G Landan, GP Raghava, I Walle Van, J Kim, J Stoye, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JD Thompson, JH Havgaard, JP Huelsenbeck, K Mizuguchi, LA Stebbings, M Anisimova, M Pop, MR Aniba, P Gardner, RA Cartwright, RB Russell, RC Edgar, RC Edgar, SA Berger, SF Altschul, T Golubchik, T Koestler, T Lassmann, T Lassmann, T Lassmann, W Fletcher   +49 more
core   +2 more sources