Results 251 to 260 of about 11,236,914 (284)

A Consensus Method for Ancestral Recombination Graphs

Journal of Molecular Evolution, 2017
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call "threshold consensus," treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the ...
Mary K. Kuhner, Jon Yamato
openaire   +2 more sources

Assessing ancestral genome reconstruction methods by resampling

2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014
Inference of ancestral or extinct genomes is important in evolutionary biology, cancer research and many other research areas. Whole-genome data has become readily available due to advances in large-scale sequencing technology. During the past decades, a number of evolutionary models and related algorithms have been designed to infer ancestral genome ...
Jun Zhou, Fei Hu, William Hoskins, Jijun Tang   +3 more
openaire   +1 more source

Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction

Journal of Combinatorial Optimization, 2009
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Louxin Zhang
exaly   +3 more sources

SBEARS—a site-based method to estimate ancestral ranges of species

Evolution; International Journal of Organic Evolution
Abstract Assessing the geographic dimension of diversification is paramount to integrate macroecology and macroevolution. Estimating ancestral ranges of species from phylogenies and spatial distribution of extant species has been fundamental for historical biogeography and can help in this endeavor.
Renan Maestri, Caetano D S, Gabriel Nakamura   +2 more
exaly   +3 more sources

Reconstruction of ancestral sequences by the inferential method, a tool for protein engineering studies

Journal of Molecular Evolution, 1994
This paper describes the inferential method, an approach for reconstructing protein and nucleotide sequences of ancestral species, starting from known, homologous, contemporary sequences. The method requires knowledge of the topology of the phylogenetic tree, whose nodes are the species to whom the reconstructed sequences belong.
Alberto di Donato, Giacinto Libertini
exaly   +4 more sources

Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods [PDF]

Journal of Molecular Evolution, 1997
Information about protein sequences of ancestral organisms is important for identifying critical amino acid substitutions that have caused the functional change of proteins in evolution. Using computer simulation, we studied the accuracy of ancestral amino acids inferred by two currently available methods (maximum-parsimony [MP] and maximum-likelihood [
Jianzhi Zhang, Masatoshi Nei
exaly   +3 more sources

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Journal of Computational Biology, 2010
Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their ...
Chauve, Cedric, Gavranovic, Haris, Ouangraoua, Aida, Tannier, Eric   +3 more
openaire   +4 more sources

Tracing Ancestral Specificity of Lectins: Ancestral Sequence Reconstruction Method as a New Approach in Protein Engineering

2014
Protein evolution is a process of molecular design leading to the diversity of functional proteins found in nature. Recent advances in bioinformatics and structural biology, in addition to recombinant protein expression techniques, enable us to analyze more directly the molecular evolution of proteins by a new method using ancestral sequence ...
Tomohisa, Ogawa, Tsuyoshi, Shirai
openaire   +2 more sources

Ancestral Sequence Reconstruction: Methods and Applications

2019
A major goal in the study of molecular evolution is to elucidate properties of ancestral proteins and to understand their adaption induced by changes in the environment. Due to the lack of macromolecular fossils, ancestral sequence reconstruction (ASR) is the only alternative to deduce sequences for evolutionary precursors of extant proteins.
openaire   +1 more source

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

2009
In 2006, a debate has risen on the question of the efficiency of bioinformatics methods to reconstruct mammalian ancestral genomes. Three years later, Gordon et al. (PLoS Genetics, 5(5), 2009) chose not to use automatic methods to build up the genome of a 100 million year old Saccharomyces cerevisiae ancestor.
openaire   +3 more sources