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. +5 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.
Bakis, Yasin +11 more
core +2 more sources
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
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences [PDF]
Journal of Computational Biology, 2007 Despite considerable efforts, it remains difficult to obtain accurate multiple sequence alignments. By using additional hits from database search of the input sequences, a few strategies have been proposed to significantly improve alignment accuracy, including the construction of profiles from the hits while performing profile alignment, the inclusion ...
Yue, Lu, Sing-Hoi, Sze
openaire +2 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 +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
doaj +1 more source
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
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
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
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 +51 more
core +5 more sources