[HTML][HTML] WormBase ParaSite− a comprehensive resource for helminth genomics
The number of publicly available parasitic worm genome sequences has increased
dramatically in the past three years, and research interest in helminth functional genomics is …
dramatically in the past three years, and research interest in helminth functional genomics is …
Recent developments in the MAFFT multiple sequence alignment program
K Katoh, H Toh - Briefings in bioinformatics, 2008 - academic.oup.com
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …
have long been and are still important issues in bioinformatics. To rapidly construct a …
Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children
Most studies of adaptive immunity to SARS-CoV-2 infection focus on peripheral blood, which
may not fully reflect immune responses at the site of infection. Using samples from 110 …
may not fully reflect immune responses at the site of infection. Using samples from 110 …
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Abstract eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at
different taxonomic levels, each with integrated and summarized functional annotations …
different taxonomic levels, each with integrated and summarized functional annotations …
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
The genus Oryza is a model system for the study of molecular evolution over time scales
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …
Whole-genome analyses resolve early branches in the tree of life of modern birds
To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Abstract Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically
and economically relevant edible marine bivalve, highly invasive and resilient to biotic and …
and economically relevant edible marine bivalve, highly invasive and resilient to biotic and …
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
K Katoh, DM Standley - Bioinformatics, 2016 - academic.oup.com
Motivation: We present a new feature of the MAFFT multiple alignment program for
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …
Ensembl comparative genomics resources
J Herrero, M Muffato, K Beal, S Fitzgerald, L Gordon… - Database, 2016 - academic.oup.com
Evolution provides the unifying framework with which to understand biology. The coherent
investigation of genic and genomic data often requires comparative genomics analyses …
investigation of genic and genomic data often requires comparative genomics analyses …
Template-based protein structure modeling using the RaptorX web server
A key challenge of modern biology is to uncover the functional role of the protein entities that
compose cellular proteomes. To this end, the availability of reliable three-dimensional …
compose cellular proteomes. To this end, the availability of reliable three-dimensional …