[HTML][HTML] Homoeologs: what are they and how do we infer them?
The evolutionary history of nearly all flowering plants includes a polyploidization event.
Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs' …
Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs' …
Ensembl 2013
Abstract The Ensembl project (http://www. ensembl. org) provides genome information for
sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat …
sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat …
Extensive error in the number of genes inferred from draft genome assemblies
JF Denton, J Lugo-Martinez, AE Tucker… - PLoS computational …, 2014 - journals.plos.org
Current sequencing methods produce large amounts of data, but genome assemblies based
on these data are often woefully incomplete. These incomplete and error-filled assemblies …
on these data are often woefully incomplete. These incomplete and error-filled assemblies …
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
Abstract The Orthologous Matrix (OMA) project is a method and associated database
inferring evolutionary relationships amongst currently 1706 complete proteomes (ie the …
inferring evolutionary relationships amongst currently 1706 complete proteomes (ie the …
Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates
Chemoreception is a widespread biological function that is essential for the survival,
reproduction, and social communication of animals. Though the molecular mechanisms …
reproduction, and social communication of animals. Though the molecular mechanisms …
Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes
Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays
and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing …
and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing …
PEP_scaffolder: using (homologous) proteins to scaffold genomes
BH Zhu, YN Song, W Xue, GC Xu, J Xiao… - …, 2016 - academic.oup.com
Motivation: Recovering the gene structures is one of the important goals of genome
assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene …
assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene …
Scaffolding low quality genomes using orthologous protein sequences
Motivation: The ready availability of next-generation sequencing has led to a situation where
it is easy to produce very fragmentary genome assemblies. We present a pipeline, SWiPS …
it is easy to produce very fragmentary genome assemblies. We present a pipeline, SWiPS …
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Motivation As the time and cost of sequencing decrease, the number of available genomes
and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene …
and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene …
Phylogenetic approaches for detecting fragmentation in genome and transcriptome annotations
I Pilizota - 2020 - discovery.ucl.ac.uk
The landscape of biological research and innovation has been transformed with the
invention of genome sequencing methods and corresponding assembly and annotation …
invention of genome sequencing methods and corresponding assembly and annotation …