{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T20:17:28Z","timestamp":1774729048485,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2018,6,5]],"date-time":"2018-06-05T00:00:00Z","timestamp":1528156800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000741","name":"The University of Warwick","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000741","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Biotechnological and Biological"},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Councils","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["EP\/L016494\/1"],"award-info":[{"award-number":["EP\/L016494\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre for Doctoral Training in Synthetic Biology"},{"name":"SynBioCDT","award":["BB\/K003240\/2"],"award-info":[{"award-number":["BB\/K003240\/2"]}]},{"name":"SynBioCDT","award":["BB\/M017982\/1"],"award-info":[{"award-number":["BB\/M017982\/1"]}]},{"name":"Warwick Integrative Synthetic Biology Centre"},{"name":"WISB"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open\u2013source R package designed for query\u2013based analysis of functional units in [meta]genomes and\/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualization and analysis tools and facilitates KEGG\u2019s flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user\u2013specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MetQy R package is freely available and can be downloaded from our group\u2019s website (http:\/\/osslab.lifesci.warwick.ac.uk) or GitHub (https:\/\/github.com\/OSS-Lab\/MetQy).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty447","type":"journal-article","created":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T15:12:34Z","timestamp":1527865954000},"page":"4134-4137","source":"Crossref","is-referenced-by-count":12,"title":["MetQy\u2014an R package to query metabolic functions of genes and genomes"],"prefix":"10.1093","volume":"34","author":[{"given":"Andrea S","family":"Martinez-Vernon","sequence":"first","affiliation":[{"name":"Synthetic Biology Centre for Doctoral Training"},{"name":"School of Life Sciences"},{"name":"Warwick Integrative Synthetic Biology (WISB) Centre, Life Sciences Building, University of Warwick, Coventry CV4 7AL, UK"}]},{"given":"Frederick","family":"Farrell","sequence":"additional","affiliation":[{"name":"School of Life Sciences"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9504-3796","authenticated-orcid":false,"given":"Orkun S","family":"Soyer","sequence":"additional","affiliation":[{"name":"Synthetic Biology Centre for Doctoral Training"},{"name":"School of Life Sciences"},{"name":"Warwick Integrative Synthetic Biology (WISB) Centre, Life Sciences Building, University of Warwick, Coventry CV4 7AL, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,6,5]]},"reference":[{"key":"2023012712315163400_bty447-B1","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/S0168-9525(97)01223-7","article-title":"A database for post-genome analysis","volume":"13","author":"Kanehisa","year":"1997","journal-title":"Trends Genet"},{"key":"2023012712315163400_bty447-B2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023012712315163400_bty447-B3","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol"},{"key":"2023012712315163400_bty447-B4","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712315163400_bty447-B5","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4134\/48921282\/bioinformatics_34_23_4134.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4134\/48921282\/bioinformatics_34_23_4134.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:18:39Z","timestamp":1674807519000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/23\/4134\/5033387"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,5]]},"references-count":5,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2018,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty447","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/215525","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,12,1]]},"published":{"date-parts":[[2018,6,5]]}}}