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Restauro-G:A Rapid Genome Re-Annotation System for Comparative Genomics

Genomics, Proteomics & Bioinformatics 2007年第1期5卷 53-58页

作者： Satoshi Tamaki Kazuharu Arakawa Nobuaki Kono Masaru Tomita Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan Department of Environ-mental Information Keio University Fujisawa 252-8520 Japan Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan

of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLASTLike Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http：//***/ under the GNU General Public License.

关键词： bioinformatics software annotation G-language Genome Analysis Environment complete genomes

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Identification of diverse novel genomoviruses in gut of wild birds

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Biosafety and Health 2021年第3期3卷 136-141页

作者： Yuxin Yao Haisheng Wu Guangming Sun Shixing Yang Quan Shen Xiaochun Wang Wen Zhang School of Medicine Jiangsu UniversityZhenjiang 212013China Qinghai institute for endemic disease prevention and control Xining 811602China Xuzhou Central Hospital 131 Huanchen RoadXuzhou 221009China

Genomoviridae is a virus family belonging to circular replication associated protein encoding ssDNA(CRESS-DNA)viruses,which have diverse genomic architecture and are widely distributed among different *** this study,we characterized 39 novel genomovirus genomes including 3 from wild egrets,9 from wild cranes,as well as 27 from wild finches in three different types of cloacal swabs of wild bird sampled in the station of Xinqing bird ringing,Maoershan Nature Reserve in Heilongjiang Province,Changbai Mountain in Jilin Province,and Hangzhou Wetland Park in Zhejiang Province,***,using a Rep sequence phylogeny-based analysis,we divided the 39 genomoviruses into 8 genera within the family Genomoviridae,including Gemycircularvirus(n=20),Gemykibivirus(n=3),Gemygorvirus(n=2),Gemyvongvirus(n=2),Gemykolovirus(n=3),Gemykrogvirus(n=6),Gemytondvirus(n=1),Gemyduguivirus(n=1)and one unclassified *** 39 genomovirus genomes belong to 36 species(27 of which are new)based on the currently accepted genomovirus pairwise nucleotide sequence identity species demarcation threshold of 78%.Overall,the research enriches our knowledge of CRESS-DNA viral diversity in China and emphasizes the prevalence of genomoviruses in nature.

关键词： CRESS-DNA virus Genomovirus Egret Crane Finch complete genomes

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