Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways.

Trung Huynh,Sen Xu

doi:10.12688/f1000research.14012.2

Abstract

We developed a Gene Annotation Easy Viewer (GAEV) that integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server. GAEV generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to. Via links to KEGG pathway maps, users can directly examine the interaction between gene products involved in the same molecular pathway. We provide a usage example by annotating the newly published freshwater microcrustacean Daphnia pulex genome. This gene-centered view of gene function and pathways will greatly facilitate the genome annotation of non-model species and metagenomics data. GAEV runs on a Windows or Linux system equipped with Python 3 and provides easy accessibility to users with no prior Unix command line experience.

Highlights

In our efforts to de novo assemble a draft genome, describing the biological function of computationally annotated genes and the molecular pathways formed by these genes’ products is critical for identifying the genetic basis of the various unique biological attributes of the species in question
It is possible to annotate the molecular functions of a set of genes from complete/partial genome assembly or metagenomics dataset and their encoded molecular pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG) automatic annotation services that are provided through webservers BlastKOALA and GhostKOALA (Kanehisa et al, 2016b)
The annotation results consist of KEGG Orthology (KO) numbers for each gene, genes mapped to KEGG pathway database, and genes mapped to BRITE

Summary

Introduction

In our efforts to de novo assemble a draft genome, describing the biological function of computationally annotated genes and the molecular pathways formed by these genes’ products is critical for identifying the genetic basis of the various unique biological attributes (e.g., physiology, life history, behavior) of the species in question. For a non-model species, we can use KAAS (KEGG Automatic Annotation Server) web services to annotate the complete or random set of genes to describe their molecular function and map them into identified molecular pathways. To provide a means to utilizing the highly informative resources at KEGG for annotating genomic sequences and molecular pathways for non-model species, we have developed a Gene Annotation Easy Viewer (GAEV) for integrating results of KEGG orthology annotation and KEGG pathways mapping using KEGG API tools in both Windows and Linux environment. GAEV is aimed to provide a gene-centered view of gene function and pathways, i.e., the complete summary of gene function and all possibly associated molecular pathways for each gene This is distinct from other KEGG-related software such as MEGAN (Huson et al, 2016) and MinPath (Ye & Doak, 2009). GAEV is implemented in Python 3 and can be used as an independent package

Methods

Conclusions