Results 21 to 30 of about 1,261,273 (206)

On the Complexity of Multiple Sequence Alignment [PDF]

Journal of Computational Biology, 1994
We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.
Tao Jiang, Lusheng Wang
openaire   +2 more sources

Bootstrapping Lexical Choice via Multiple-Sequence Alignment [PDF]

, 2002
An important component of any generation system is the mapping dictionary, a lexicon of elementary semantic expressions and corresponding natural language realizations.
Barzilay, Regina, Lee, Lillian
core   +7 more sources

Multiple sequence alignments in linguistics [PDF]

Proceedings of the EACL 2009 Workshop on Language Technology and Resources for Cultural Heritage, Social Sciences, Humanities, and Education - LaTeCH-SHELT&R '09, 2009
In this study we apply and evaluate an iterative pairwise alignment program for producing multiple sequence alignments, ALPHAMALIG (Alonso et al., 2004), using as material the phonetic transcriptions of words used in Bulgarian dialectological research. To evaluate the quality of the multiple alignment, we propose two new methods based on comparing each
Martijn Wieling, John Nerbonne, Jelena Prokić   +2 more
openaire   +3 more sources

Enhanced Genetic Method for Optimizing Multiple Sequence Alignment

Mathematics, 2023
In the realm of bioinformatics, Multiple Sequence Alignment (MSA) is a pivotal technique used to optimize the alignment of multiple biological sequences, guided by specific scoring criteria.
Mohammed K. Ibrahim, Umi Kalsom Yusof, Taiseer Abdalla Elfadil Eisa, Maged Nasser   +3 more
doaj   +1 more source

Evolutionary distances in the twilight zone -- a rational kernel approach [PDF]

, 2010
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.
A Keller, A Löytynoja, A Stamatakis, B Chor, B Schölkopf, Benjamin Merget, C Cortes, C Daskalakis, CB Do, E Rivas, F Bemm, Florian Markowetz, Frank Förster, G Talavera, HH Otu, I Ulitsky, J Felsenstein, J Friedrich, J Hein, JL Thorne, JL Thorne, Jörg Schultz, KM Wong, LS Wang, M Höhl, M Höhl, M Mohri, M Mohri, M Wolf, MA Buchheim, MA Suchard, Matthias Wolf, MJ Bishop, MK Kuhner, MS Waterman, N Goldman, N Higham, R Durbin, RC Edgar, RF Doolittle, Roland F. Schwarz, S Roch, S Whelan, SR Eddy, T Mailund, T Müller, TH Ogden, V Levenshtein, W Fletcher, W Fletcher, Wayne Delport, William Fletcher   +51 more
core   +4 more sources

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

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
doaj   +1 more source

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, Szabó Adrienn, Miklós István, Hein Jotun   +3 more
doaj   +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, Raghava GPS, Audley Patrick C, Barber Jonathan D, Barton Geoffrey J   +4 more
doaj   +1 more source

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., Bloom, Jesse D., Endelman, Jeffrey B., Hiraga, Kaori, Landwehr, Marco, Otey, Christopher R.   +5 more
core   +1 more source