Database resources of the national center for biotechnology information
Abstract The National Center for Biotechnology Information (NCBI) produces a variety of
online information resources for biology, including the GenBank® nucleic acid sequence …
online information resources for biology, including the GenBank® nucleic acid sequence …
Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health
JC Ezeji, DK Sarikonda, A Hopperton, HL Erkkila… - Gut …, 2021 - Taylor & Francis
Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-
negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous …
negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous …
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
M Uliano-Silva, JGRN Ferreira, K Krasheninnikova… - BMC …, 2023 - Springer
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb)
and highly accurate (> Q20). Because of these properties, they have revolutionised genome …
and highly accurate (> Q20). Because of these properties, they have revolutionised genome …
TimeTree 5: an expanded resource for species divergence times
We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the
timetree of life project that aims to synthesize published molecular timetrees and make …
timetree of life project that aims to synthesize published molecular timetrees and make …
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …
can only capture few abundant organisms from most metagenomes. Here we present …
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity
D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic Acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool
Abstract The Interactive Tree Of Life (https://itol. embl. de) is an online tool for the
management, display, annotation and manipulation of phylogenetic and other trees. It is …
management, display, annotation and manipulation of phylogenetic and other trees. It is …
BUSCO: assessing genomic data quality and beyond
Abstract Evaluation of the quality of genomic “data products” such as genome assemblies or
gene sets is of critical importance in order to recognize possible issues and correct them …
gene sets is of critical importance in order to recognize possible issues and correct them …
Protein complex prediction with AlphaFold-Multimer
While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
Abstract The Genome Taxonomy Database (GTDB; https://gtdb. ecogenomic. org) provides a
phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic …
phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic …