AGeS: A Software System for Microbial Genome Sequence Annotation

Background
The annotation of genomes from next-generation sequencing platforms needs to
be rapid, high-throughput, and fully integrated and automated. Although a
few Web-based annotation services have recently become available, they may
not be the best solution for researchers that need to annotate a large
number of genomes, possibly including proprietary data, and store them
locally for further analysis. To address this need, we developed a
standalone software application, the Annotation of microbial Genome
Sequences (AGeS) system, which incorporates publicly available and
in-house-developed bioinformatics tools and databases, many of which are
parallelized for high-throughput performance.
Methodology
The AGeS system supports three main capabilities. The first is the storage of
input contig sequences and the resulting annotation data in a central,
customized database. The second is the annotation of microbial genomes using
an integrated software pipeline, which first analyzes contigs from
high-throughput sequencing by locating genomic regions that code for
proteins, RNA, and other genomic elements through the Do-It-Yourself
Annotation (DIYA) framework. The identified protein-coding regions are then
functionally annotated using the in-house-developed Pipeline for Protein
Annotation (PIPA). The third capability is the visualization of annotated
sequences using GBrowse. To date, we have implemented these capabilities for
bacterial genomes. AGeS was evaluated by comparing its genome annotations
with those provided by three other methods. Our results indicate that the
software tools integrated into AGeS provide annotations that are in general
agreement with those provided by the compared methods. This is demonstrated
by a >94% overlap in the number of identified genes, a significant
number of identical annotated features, and a >90% agreement in
enzyme function predictions.