Table 1 Genome annotation pipelines
From: Recent advances in genome annotation and synthetic biology for the development of microbial chassis
Pipeline name | Details | Source | URL |
|---|---|---|---|
PGAP | An automatic prokaryotic genome annotation pipeline, which is a set of computational tools and algorithms that are used to predict the presence and location of genes in the genome of a prokaryotic organism | Â [63] | |
Prokka v1.14.6 | A software tool for rapidly annotating genomes, which uses external feature prediction tools like RNAmmer and Prodigal to identify the coordinates of genomic features within contigs | [61] | |
RAST | A fully automated pipeline for annotating bacterial and archaeal genomes | [10] | |
MicrobeAnnotator | A tool that predicts all types of prokaryotic genes from a single or a set of anonymous genomic sequences of varying lengths. This tool is commonly used in the analysis of prokaryotic genomes | [58] | |
EggNOG-mapper v2.1.9 | A tool for automatically annotating the function of genes based on precomputed orthology assignments | [13] | |
DRAM | A tool that uses databases like KEGG and PFAM to organize microbial genomic information into a catalog of microbial traits | [62] | |
DFAST | A pipeline that supports genome submission to the public database DNA Data Bank of Japan (DDBJ) using the GHOSTX algorithm | [67] | |
GenSAS | An online pipeline that provides structural and functional annotations of genomic sequences | [28] | |
BlastKOALA | A tool that carries out automated annotation of fully sequenced genomes by using KEGG's internal annotation tool, KOALA, to assign K numbers to KEGG genes using SSEARCH computation | [33] |