{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T15:08:55Z","timestamp":1760800135756,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100009344","name":"Agouron Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009344","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000008","name":"David and Lucile Packard Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000008","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NASA Exobiology","award":["NNX16AJ57G"],"award-info":[{"award-number":["NNX16AJ57G"]}]},{"name":"Society in Science\u2013Branco Weiss"},{"DOI":"10.13039\/501100003006","name":"ETH Zurich","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genome-resolved metagenomics allows the construction of draft microbial genomes from short-read shotgun metagenomics (Metagenome-Assembled Genomes, or MAGs); however, even high-quality MAGs are typically somewhat incomplete and contain a small amount of contaminant sequence, making accurate prediction of metabolic potential challenging. Here, we describe MetaPOAP, an algorithm for probabalistic assessment of the statistical likelihoods for the presence or absence of metabolic pathways in MAGs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MetaPOAP is available as Python scripts on GitHub or from the Fischer lab webpage, https:\/\/github.com\/lmward\/MetaPOAP.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty510","type":"journal-article","created":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T20:27:46Z","timestamp":1529526466000},"page":"4284-4286","source":"Crossref","is-referenced-by-count":38,"title":["MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9290-2567","authenticated-orcid":false,"given":"Lewis M","family":"Ward","sequence":"first","affiliation":[{"name":"Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA"}]},{"given":"Patrick M","family":"Shih","sequence":"additional","affiliation":[{"name":"Environmental Genomics and Systems Biology Division, E O Lawrence Berkeley National Laboratory, Berkeley, CA"},{"name":"Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA"},{"name":"Department of Plant Biology, University of California, Davis, CA, USA"}]},{"given":"Woodward W","family":"Fischer","sequence":"additional","affiliation":[{"name":"Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,6,22]]},"reference":[{"key":"2023012712254786700_bty510-B1","article-title":"Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle","volume":"1","author":"Anantharaman","year":"2018","journal-title":"ISME J"},{"key":"2023012712254786700_bty510-B2","doi-asserted-by":"crossref","first-page":"75.","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012712254786700_bty510-B3","doi-asserted-by":"crossref","first-page":"725.","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol"},{"key":"2023012712254786700_bty510-B4","doi-asserted-by":"crossref","first-page":"3390","DOI":"10.1093\/nar\/gki615","article-title":"Protein length in eukaryotic and prokaryotic proteomes","volume":"33","author":"Brocchieri","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023012712254786700_bty510-B5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012712254786700_bty510-B6","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1126\/science.aao2410","article-title":"Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium","volume":"359","author":"Mall","year":"2018","journal-title":"Science"},{"key":"2023012712254786700_bty510-B501","doi-asserted-by":"crossref","DOI":"10.1201\/9780429258770","author":"Milo","year":"2015","journal-title":"Cell Biology by the Numbers"},{"key":"2023012712254786700_bty510-B7","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1126\/science.aao3407","article-title":"A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile","volume":"359","author":"Nunoura","year":"2018","journal-title":"Science"},{"key":"2023012712254786700_bty510-B8","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"2023012712254786700_bty510-B9","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol"},{"key":"2023012712254786700_bty510-B10","doi-asserted-by":"crossref","first-page":"260","DOI":"10.3389\/fmicb.2018.00260","article-title":"Evolution of phototrophy in the Chloroflexi phylum driven by horizontal gene transfer","volume":"9","author":"Ward","year":"2018","journal-title":"Front. Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/24\/4284\/48921014\/bioinformatics_34_24_4284.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/24\/4284\/48921014\/bioinformatics_34_24_4284.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:12:24Z","timestamp":1674825144000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/24\/4284\/5043007"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,22]]},"references-count":11,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2018,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty510","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,12,15]]},"published":{"date-parts":[[2018,6,22]]}}}