From: Recent advances in genome annotation and synthetic biology for the development of microbial chassis
Tool | Description | Source |
---|---|---|
(Meta)GeneMark | A webpage that provides access to gene prediction in metagenomes | [24] |
(Meta)Prodigal | Gene prediction software that is used to identify protein-coding genes in prokaryotic genomes | [29] |
MetaGeneAnnotator | Predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths | [47] |
CDD | Comprises protein domains conserved throughout molecular evolution | [41] |
ChEBI | The CHEBI database contains manually curated data on chemical entities | [26] |
GO FEAT | A web-based functional annotation tool for genomic and transcriptomic data | [5] |
GO | The Gene Ontology database provides a standardized vocabulary for describing gene function | |
KEGG | Links genomic data and higher-order functional information | [32] |
Rhea | Rhea is a database that contains functional annotations for enzymes and descriptions of metabolic pathways. The annotations in Rhea are based on expert-curated, non-redundant information on biochemical reactions | [43] |
InterPro | InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites | [53] |
NCBI Blast | BLAST is a program that identifies regions of similarity between sequences | [30] |
SEED | The SEED database provides genome annotations across thousands of genomes | [52] |
UniProt | A freely accessible resource on protein sequences and functional annotation | [11] |
RefSeq | RefSeq provides a well-annotated set of sequences, including genomic DNA, transcripts, and proteins | [48] |
FunMappOne | FunMappOne is a tool for functional analysis and visualization of gene lists | [60] |
g:Profiler | Web server for functional enrichment analysis and additional information mining | [37] |
GAEV | A tool that was developed for the construction of complete sets of molecular pathways for non-model organisms using KEGG gene function annotations | [73] |
GOPlot | GOPlot is an R package for the functional analysis of gene lists | [69] |