BEACON: automated tool for Bacterial GEnome Annotation ComparisON
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Permanent link to this recordhttp://hdl.handle.net/10754/575255
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AbstractBackground Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/
CitationBEACON: automated tool for Bacterial GEnome Annotation ComparisON 2015, 16 (1) BMC Genomics
PublisherSpringer Science + Business Media
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Showing items related by title, author, creator and subject.
PanoAnnotatorYang, Shang Ta; Peng, Chi-Han; Wonka, Peter; Chu, Hung Kuo (SIGGRAPH Asia 2018 Posters on - SA '18, ACM Press, 2018-11-30) [Conference Paper]We present PanoAnnotator, a semi-automatic system that facilitates the annotation of 2D indoor panoramas to obtain high-quality 3D room layouts. Observing that fully-automatic methods are often restricted to a subset of indoor panoramas and generate room layouts with mediocre quality, we instead propose a hybrid method to recover high-quality room layouts by leveraging both automatic estimations and user edits. Specifically, our system first employs state-of-the-art methods to automatically extract 2D/3D features from input panorama, based on which an initial Manhattan world layout is estimated. Then, the user can further edit the layout structure via a set of intuitive operations, while the system will automatically refine the geometry according to the extracted features. The experimental results show that our automatic initialization outperforms a selected fully-automatic state-of-the-art method in producing room layouts with higher accuracy. In addition, our complete system reduces annotation time when comparing with a fully-manual tool for achieving the same high quality results.
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