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Software System for Microbial Genome Sequence Annotation

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.

A standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. AGeS was designed to support three main capabilities. The first is the storage of input contig sequences in FASTA format and the resulting annotation data in a central, customized database, where the data manipulation and visualization steps are performed through easy-to-use graphical user interfaces (GUIs). The second is the annotation of microbial genomes using an integrated software pipeline, which analyzes sequence contigs and locates genomic regions that code for proteins, RNAs, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then annotated using an in-house-developed, high-throughput pipeline, the Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using the opensource genome browser GBrowse. Full genome and protein annotation, storage, and visualization for bacterial genomes have been implemented.

The AGeS system was designed and implemented to provide a standalone, integrated solution that users can install on their computers. AGeS can be installed on either a standalone Linux computer or a Linux cluster. When run on a multicore Linux computer or a Linux cluster, AGeS supports OpenMPI for parallel execution and PBS for batch submission. The AGeS system has been designed for easy integration with future sequence analysis modules. Its Web applications use technologies based on open standards, including Java, JavaScript, and XML.

This work was done by Kamal Kumar, Valmik Desai, Li Cheng, Maxim Khitrov, Deepak Grover, Ravi Vijaya Satya, Chenggang Yu, Nela Zavaljevski, and Jaques Reifman of the Army Medical Research and Materiel Command. ARL-0129

Topics:
Bacteria Biological sciences Computer software and hardware Human machine interface (HMI) Imaging and visualization Materials handling Optics Software Storage
This Brief includes a Technical Support Package (TSP).
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AGeS: A Software System for Microbial Genome Sequence Annotation

(reference ARL-0129) is currently available for download from the TSP library.

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    Defense Tech Briefs Magazine

    This article first appeared in the December, 2011 issue of Defense Tech Briefs Magazine (Vol. 5 No. 6).

    Read more articles from this issue here.

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    Overview

    The document presents the Annotation of microbial Genome Sequences (AGeS) software system, developed to address the growing need for rapid, high-throughput, and fully automated genome annotation following the exponential increase in available genome sequences due to advancements in DNA sequencing technologies. AGeS is designed specifically for annotating microbial genomes, incorporating both publicly available and in-house-developed bioinformatics tools and databases.

    AGeS supports three main capabilities:

    1. Data Storage: It allows for the storage of input contig sequences in FASTA format and the resulting annotation data in a centralized, customized database. This facilitates easy data manipulation and visualization through user-friendly graphical user interfaces (GUIs).

    2. Genome Annotation: The software employs an integrated pipeline that analyzes sequence contigs to identify genomic regions coding for proteins, RNAs, and other elements. This is achieved through the Do-It-Yourself Annotation (DIYA) framework, which locates these regions, followed by functional annotation of the identified protein-coding regions using the Pipeline for Protein Annotation (PIPA).

    3. Visualization: AGeS includes capabilities for visualizing annotated sequences using the open-source genome browser GBrowse, enhancing the accessibility and interpretability of the data.

    The document highlights the evaluation of AGeS by comparing its genome annotations with those from three other methods. The results indicate a high level of agreement, with over 94% overlap in the number of identified genes and more than 90% agreement in enzyme function predictions. This demonstrates the reliability and effectiveness of the tools integrated within AGeS.

    The authors express gratitude to the developers of various open-source bioinformatics tools that contributed to the AGeS pipeline, emphasizing the collaborative nature of bioinformatics research. The document concludes with acknowledgments and a note on the authors' affiliations, ensuring that the opinions expressed are their own and do not reflect official views of the U.S. Army or the Department of Defense.

    Overall, AGeS represents a significant advancement in microbial genome annotation, providing researchers with a comprehensive, efficient, and user-friendly tool for genomic analysis, which is crucial for applications in diagnostics, vaccine development, and comparative genomics.

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