{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T07:23:29Z","timestamp":1781767409857,"version":"3.54.5"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2018,9,4]],"date-time":"2018-09-04T00:00:00Z","timestamp":1536019200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Research Council Research","award":["ERC-2012-StG311000"],"award-info":[{"award-number":["ERC-2012-StG311000"]}]},{"name":"Science Foundation Ireland Fellowship","award":["17\/IFA\/5303"],"award-info":[{"award-number":["17\/IFA\/5303"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>A number of limiting factors mean that traditional genome annotation tools either fail or perform sub-optimally when trying to detect coding sequences in poor quality genome assemblies\/genome reports. This means that potentially useful data is accessible only to those with specific skills and expertise in assembly and annotation. We present an Assembled-Genome mIning pipeLinE (AGILE) written in Perl that combines bioinformatics tools with a number of steps to overcome the limitations imposed by such assemblies when applied to highly fragmented genomes. Our methodology uses user-specified query genes from a closely related species to mine and annotate coding sequences that would traditionally be missed by standard annotation packages. Despite a focus on mammalian genomes, the generalized implementation means that it may be applied to any genome assembly, providing a means for non-specialists to gather gene sequences for downstream analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and associated files are available at: https:\/\/github.com\/batlabucd\/GenomeMining and https:\/\/bitbucket.org\/BatlabUCD\/genomemining\/src. Singularity and Virtual Box images available at https:\/\/figshare.com\/s\/a0004bf93dc43484b0c0.<\/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\/bty781","type":"journal-article","created":{"date-parts":[[2018,9,3]],"date-time":"2018-09-03T12:44:09Z","timestamp":1535978649000},"page":"1252-1254","source":"Crossref","is-referenced-by-count":7,"title":["AGILE: an assembled genome mining pipeline"],"prefix":"10.1093","volume":"35","author":[{"given":"Graham M","family":"Hughes","sequence":"first","affiliation":[{"name":"School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma C","family":"Teeling","sequence":"additional","affiliation":[{"name":"School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,4]]},"reference":[{"key":"2023013107274883300_bty781-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023013107274883300_bty781-B2","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1101\/gr.6743907","article-title":"Maker: an easy-to-use annotation pipeline designed for emerging model organism genomes","volume":"18","author":"Cantarel","year":"2008","journal-title":"Genome Res"},{"key":"2023013107274883300_bty781-B3","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1093\/molbev\/msu132","article-title":"OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals","volume":"31","author":"Douzery","year":"2014","journal-title":"Mol. 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