ages a software system for microbial genome sequence annotation年龄微生物基因组序列注释的软件系统.pdfVIP

AGeS: A Software System for Microbial Genome Sequence Annotation Kamal Kumar, Valmik Desai, Li Cheng, Maxim Khitrov, Deepak Grover, Ravi Vijaya Satya, Chenggang Yu, Nela Zavaljevski, Jaques Reifman* DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, Maryland, United States of America Abstract 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 GBrows