[PDF] eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale | Semantic Scholar (2024)

This work demonstrates that structural similarity is more powerful to generate functional prediction and annotation than sequence alone, bridging longer evolutionary distances.

It is demonstrated that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify hom*ologous proteins over long evolutionary distances, and will be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.

The eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels.

An easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format is developed.

The newest version of MATEdb (MATEdb2) is presented, a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla that overcomes some of the previous limitations of the database and provides gene annotations from genomes obtained using the same pipeline.

This work presents metashot/aweMAGs, a fully automated workflow capable of performing quality assessment, annotation and phylogenomic placement of eukaryotic MAGs, and can run out-of-the-box on any platform that supports Docker, Singularity and Nextflow, including computing clusters or batch systems in the cloud.

A new approach for classifying proteins into a taxonomy of functions and IDTAXA is developed, which was more accurate than BLAST or HMMER at assigning sequences to KEGG ortholog groups and demonstrated its utility for genome annotation.

This work presents Metazoan Assemblies from Transcriptomic Ensembles (MATEdb), a curated database of 335 high-quality transcriptome assemblies from different animal phyla analyzed following the same pipeline, totalling 423 high- quality genomic and transcriptomic data sets.

To predict gene functions in bacteria, SAP is developed, a novel synteny-aware gene function prediction tool based on protein embeddings from state-of-the-art protein language models that leverages the unique operon structure of bacteria through conserved synteny.

...

...

EggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from eggNOG, benchmarked Gene Ontology predictions against two widely used hom*ology-based approaches: BLAST and InterProScan.

The presented proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database.

New content and features in the BiGG Models repository are detail, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites.

The recent advances and outstanding challenges in orthology inference are reviewed, as revealed at a symposium and meeting held at the University of Southern California in 2017.

The Blast2GO framework is used to carry out a detailed analysis of annotation behaviour through hom*ology transfer and its impact in functional genomics research to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

It is found that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils, which supports the continued use of manually curated inclusion thresholds in the Pfam database.

A new Java-based architecture for the widely used protein function prediction software package InterProScan is described, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis.

GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models.

The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes.

...

...