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Article
Biochemistry & Molecular Biology
Elodie Drula et al.
Summary: The CAZy database, freely available for browsing and download, is deeply rooted in human curation and plays a crucial role in maintaining and updating family classification, classifying new sequences, and presenting functional information. Over the past 8 years, there has been an increase in novel families and extensive annotations conducted, highlighting the significant amount of work involved in analyzing and reporting biochemical data from the literature.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Diego Fuentes et al.
Summary: PhylomeDB is a unique knowledge base that provides public access to annotated sequences, alignments, and phylogenies of homologous genes. The latest version includes a new web interface, optimized searching procedures, and a significant expansion in core data with access to 534 phylomes and relationships for genes in over 6000 species, making it the largest public repository of gene phylogenies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ziqi Deng et al.
Summary: PhyloCloud is an online platform designed to host and index large collections of phylogenetic trees, providing seamless access to analyses and operations, as well as custom annotations and multiple sequence alignments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jorge Botas et al.
Summary: GeCoViz is an online resource that provides fast and interactive visualization of custom genomic regions, allowing for easy investigation of the functional and evolutionary interpretation of prokaryotic genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Huaiyu Mi et al.
Summary: PANTHER is a resource for evolutionary and functional classification of protein-coding genes, with extensive improvements made in the past two years, including the refactoring of Protein Class ontology and addition of services for programmatic access. The resource provides comprehensive classification and annotation information for genes from different taxonomic groups and also allows users to add their own protein sequences for evolutionary context and fine-grained annotations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wenjun Li et al.
Summary: The RefSeq project at NCBI contains a vast number of bacterial and archaeal genomes and proteins, with a focus on reducing spurious annotation through the use of expanded protein family models. The Protein Family Models Entrez database provides users with access to the PFMs, supporting multi-genome analyses and connections to the literature. The reference and representative genome set of prokaryotic genomes within RefSeq is regularly recalculated and available for download and BLAST searches.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Seth Carbon et al.
Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Damian Szklarczyk et al.
Summary: The STRING database integrates various associations between proteins, including physical interactions and functional associations, by collecting evidence from sources such as literature, databases, computational predictions, and systematic transfers. STRING aims for wide coverage and provides extensive user interface features and querying methods for experimental data.
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Biochemistry & Molecular Biology
Alex Bateman et al.
Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.
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(2021)
Article
Biochemistry & Molecular Biology
Evgeny M. Zdobnov et al.
Summary: OrthoDB provides evolutionary and functional annotations of orthologs for a vast number of organisms, with a wide coverage of species and rich data content. The user interface has been enhanced, and features three views on the data, as well as online tools for interactive exploration and data download.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Benjamin Linard et al.
Summary: Accurate determination of evolutionary relationships between genes is crucial in biology, with homology often determined by sequence similarity analysis. However, distinguishing between orthologs and paralogs presents challenges. The recent QFO meeting in Japan highlighted progress in standardizing orthology methods and integrating orthology across different biological levels, while also revealing challenges in leveraging orthology computations and adapting methods to genomic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra et al.
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
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(2021)
Article
Biochemistry & Molecular Biology
Adrian M. Altenhoff et al.
Summary: OMA is a resource that elucidates evolutionary relationships among 2326 genes, providing functions such as pairwise and groupwise orthologs and functional annotations. The updated OMA database has been reorganized into gene-, group-, and genome-centric pages, with new features and improvements added.
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(2021)
Article
Biochemistry & Molecular Biology
Michael Y. Galperin et al.
Summary: The COG database, created in 1997 and most recently updated in 2014, includes extensive information on bacterial and archaeal genomes. The current version introduces new features and plans for future expansion and refinement of annotations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jaina Mistry et al.
Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.
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BMC BIOINFORMATICS
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JZ Zhang
TRENDS IN ECOLOGY & EVOLUTION
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Biochemistry & Molecular Biology
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Biochemistry & Molecular Biology
HM Berman et al.
NUCLEIC ACIDS RESEARCH
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