{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:19:06Z","timestamp":1792793946032,"version":"4.5.0"},"reference-count":80,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T00:00:00Z","timestamp":1725580800000},"content-version":"vor","delay-in-days":249,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/0114b2m14","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"https:\/\/ror.org\/0114b2m14","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Automated annotations of protein functions are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the underlying databases. We discuss how to use interactive tools to quickly find different kinds of information relevant to a protein\u2019s function. Many of these tools are available via PaperBLAST (http:\/\/papers.genomics.lbl.gov). Combining these tools often allows us to infer a protein\u2019s function. Ideally, accurate annotations would allow us to predict a bacterium\u2019s capabilities from its genome sequence, but in practice, this remains challenging. We describe interactive tools that infer potential capabilities from a genome sequence or that search a genome to find proteins that might perform a specific function of interest.<\/jats:p>\n                  <jats:p>Database URL: http:\/\/papers.genomics.lbl.gov<\/jats:p>","DOI":"10.1093\/database\/baae089","type":"journal-article","created":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T19:18:32Z","timestamp":1723231112000},"source":"Crossref","is-referenced-by-count":8,"title":["Interactive tools for functional annotation of bacterial genomes"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4251-0362","authenticated-orcid":false,"given":"Morgan N","family":"Price","sequence":"first","affiliation":[{"name":"Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam P","family":"Arkin","sequence":"additional","affiliation":[{"name":"Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory , 1 Cyclotron Rd, Berkeley, CA 94720, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,9,6]]},"reference":[{"key":"2024090616214106700_R1","doi-asserted-by":"publisher","first-page":"e00306","DOI":"10.1128\/mBio.00306-15","article-title":"Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons","volume":"6","author":"Wetmore","year":"2015","journal-title":"mBio"},{"key":"2024090616214106700_R2","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1038\/s41586-018-0124-0","article-title":"Mutant phenotypes for thousands of bacterial genes of unknown 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