{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,8]],"date-time":"2023-02-08T20:24:02Z","timestamp":1675887842931},"reference-count":14,"publisher":"World Scientific Pub Co Pte Lt","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:p> Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (&gt; 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (access code: \"guest\"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. <\/jats:p>","DOI":"10.1142\/s0219720008003850","type":"journal-article","created":{"date-parts":[[2008,12,17]],"date-time":"2008-12-17T06:31:28Z","timestamp":1229495488000},"page":"1193-1211","source":"Crossref","is-referenced-by-count":4,"title":["EnGenIUS \u2014 ENVIRONMENTAL GENOME INFORMATIONAL UTILITY SYSTEM"],"prefix":"10.1142","volume":"06","author":[{"given":"MIHAILO","family":"KAPLAREVIC","sequence":"first","affiliation":[{"name":"Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"ALISON E.","family":"MURRAY","sequence":"additional","affiliation":[{"name":"Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"STEPHEN C.","family":"CARY","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand"},{"name":"College of Marine and Earth Sciences, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"GUANG R.","family":"GAO","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of Delaware, 308 DuPont Hall, Newark, DE 19711, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.1.1"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.17"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-6-5"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg312"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl217"},{"key":"rf7","first-page":"34","volume":"59","author":"Kanehisa M.","journal-title":"Sci. Technol. Jpn."},{"key":"rf8","author":"Grzymski J. J.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.23.6403-6405.2002"},{"key":"rf12","first-page":"282","volume":"17","author":"Godzik A.","journal-title":"Bioinformatics"},{"key":"rf13","author":"Grzymski J. J.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh121"},{"key":"rf15","first-page":"6633","volume":"31","author":"Faraut T.","journal-title":"Nucleic. Acids. Res."},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1101\/gr.9.9.868"},{"key":"rf17","first-page":"27","volume":"20","author":"Goto S.","journal-title":"Nucleic. Acids. Res."}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720008003850","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T22:42:09Z","timestamp":1565131329000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720008003850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,12]]},"references-count":14,"journal-issue":{"issue":"06","published-online":{"date-parts":[[2011,11,21]]},"published-print":{"date-parts":[[2008,12]]}},"alternative-id":["10.1142\/S0219720008003850"],"URL":"https:\/\/doi.org\/10.1142\/s0219720008003850","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,12]]}}}