Figure 1.
Annotation of microbial Genome Sequences (AGeS) system architecture.
The Web server hosts the AGeS Web application and accepts user requests via standard Web browsers. The workflow manager handles user requests for sequence management, runs the annotation pipeline, and presents the annotation results via GBrowse visualization. The sequence database stores all sequence and job-related data.
Figure 2.
Schematic representation of the various tools of the genome annotation pipeline.
Given assembled contigs in a FASTA format file, processing starts with the Do-It-Yourself Annotation (DIYA) genome annotation tool, followed by post-processing, tandem repeat annotation, and protein function prediction with Pipeline for Protein Annotation (PIPA).
Table 1.
List of genome annotation tools incorporated in DIYA and protein annotation tools integrated in PIPA.
Table 2.
Summary of genomic features predicted by AGeS and other annotation methods for two draft genomes and one completed genome.
Table 3.
Detailed comparison of overlapping gene segments for the three analyzed genomes, displaying the number and percentage of genes in each category.
Table 4.
Comparison of enzyme protein function (EC number) predictions between AGeS and other annotation methods for the three analyzed genomes.