{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T07:26:09Z","timestamp":1767338769110,"version":"3.37.3"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T00:00:00Z","timestamp":1716768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T00:00:00Z","timestamp":1716768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Conseller\u00eda de Educaci\u00f3n, Universidades e Formaci\u00f3n Profesional","award":["ED431C 2022\/03-GRC"],"award-info":[{"award-number":["ED431C 2022\/03-GRC"]}]},{"DOI":"10.13039\/501100010801","name":"Xunta de Galicia","doi-asserted-by":"publisher","award":["TR349V"],"award-info":[{"award-number":["TR349V"]}],"id":[{"id":"10.13039\/501100010801","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04293\/2020"],"award-info":[{"award-number":["UIDB\/04293\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>The initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initial version of SEDA lacks a command-line interface for more advanced users and does not allow the creation of automated analysis pipelines.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The present paper discusses the updates of the new SEDA release, including the addition of a complete command-line interface, new functionalities like gene annotation, a framework for automated pipelines, and improved integration in Linux environments.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>SEDA is an open-source Java application and can be installed using the different distributions available (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.sing-group.org\/seda\/download.html\">https:\/\/www.sing-group.org\/seda\/download.html<\/jats:ext-link>) as well as through a Docker image (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/hub.docker.com\/r\/pegi3s\/seda\">https:\/\/hub.docker.com\/r\/pegi3s\/seda<\/jats:ext-link>). It is released under a GPL-3.0 license, and its source code is publicly accessible on GitHub (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/sing-group\/seda\">https:\/\/github.com\/sing-group\/seda<\/jats:ext-link>). The software version at the time of submission is archived at Zenodo (version v1.6.0, <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.5281\/zenodo.10201605\">http:\/\/doi.org\/10.5281\/zenodo.10201605<\/jats:ext-link>).<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05818-2","type":"journal-article","created":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T12:02:13Z","timestamp":1716811333000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines"],"prefix":"10.1186","volume":"25","author":[{"given":"Miguel","family":"Reboiro-Jato","sequence":"first","affiliation":[]},{"given":"Daniel","family":"P\u00e9rez-Rodr\u00edguez","sequence":"additional","affiliation":[]},{"given":"Miguel Jos\u00e9","family":"Da Silva","sequence":"additional","affiliation":[]},{"given":"David","family":"Vila-Fern\u00e1ndez","sequence":"additional","affiliation":[]},{"given":"Cristina P.","family":"Vieira","sequence":"additional","affiliation":[]},{"given":"Jorge","family":"Vieira","sequence":"additional","affiliation":[]},{"given":"Hugo","family":"L\u00f3pez-Fern\u00e1ndez","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,5,27]]},"reference":[{"key":"5818_CR1","doi-asserted-by":"crossref","unstructured":"Lopez-Fernandez H, Duque P, Vazquez N, Fdez-Riverola F, Reboiro-Jato M, Vieira CP, et al. SEDA: a desktop tool suite for FASTA files processing. IEEE\/ACM Trans Comput Biol Bioinform. 2020;1\u20131.","DOI":"10.1109\/TCBB.2020.3040383"},{"issue":"10","key":"5818_CR2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163962","volume":"11","author":"W Shen","year":"2016","unstructured":"Shen W, Le S, Li Y, Hu F. SeqKit: a cross-platform and ultrafast Toolkit for FASTA\/Q file manipulation. PLoS ONE. 2016;11(10): e0163962.","journal-title":"PLoS ONE"},{"key":"5818_CR3","unstructured":"Li H. lh3\/seqtk [Internet]. 2020 [cited 2020 Mar 20]. Available from: https:\/\/github.com\/lh3\/seqtk"},{"key":"5818_CR4","unstructured":"seqmagick [Internet]. [cited 2020 Mar 20]. Available from: https:\/\/fhcrc.github.io\/seqmagick\/"},{"issue":"1","key":"5818_CR5","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1745-6150-3-20","volume":"3","author":"Y Kapustin","year":"2008","unstructured":"Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct. 2008;3(1):20.","journal-title":"Biol Direct"},{"key":"5818_CR6","volume":"22","author":"KJ Hoff","year":"2018","unstructured":"Hoff KJ, Stanke M. Predicting genes in single genomes with AUGUSTUS. Curr Protoc Bioinform. 2018;22: e57.","journal-title":"Curr Protoc Bioinform"},{"key":"5818_CR7","unstructured":"pegi3s\/cga [Internet]. pegi3s; 2022 [cited 2024 Feb 14]. Available from: https:\/\/github.com\/pegi3s\/cga"},{"issue":"Web Server","key":"5818_CR8","doi-asserted-by":"publisher","first-page":"W5","DOI":"10.1093\/nar\/gkn201","volume":"36","author":"M Johnson","year":"2008","unstructured":"Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008;36(Web Server):W5-9.","journal-title":"Nucleic Acids Res"},{"key":"5818_CR9","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/978-1-59745-535-0_4","volume-title":"Plant bioinformatics","author":"E Boutet","year":"2007","unstructured":"Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. UniProtKB\/Swiss-Prot. In: Edwards D, editor. Plant bioinformatics. Totowa: Humana Press; 2007. p. 89\u2013112. https:\/\/doi.org\/10.1007\/978-1-59745-535-0_4."},{"issue":"W1","key":"5818_CR10","doi-asserted-by":"publisher","first-page":"W636","DOI":"10.1093\/nar\/gkz268","volume":"47","author":"F Madeira","year":"2019","unstructured":"Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019;47(W1):W636\u201341.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"5818_CR11","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.593","volume":"18","author":"H L\u00f3pez-Fern\u00e1ndez","year":"2021","unstructured":"L\u00f3pez-Fern\u00e1ndez H, Gra\u00f1a-Castro O, Nogueira-Rodr\u00edguez A, Reboiro-Jato M, Glez-Pe\u00f1a D. Compi: a framework for portable and reproducible pipelines. PeerJ Comput Sci. 2021;18(7): e593.","journal-title":"PeerJ Comput Sci"},{"issue":"9","key":"5818_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0204474","volume":"13","author":"H L\u00f3pez-Fern\u00e1ndez","year":"2018","unstructured":"L\u00f3pez-Fern\u00e1ndez H, Reboiro-Jato M, Glez-Pe\u00f1a D, Laza R, Pav\u00f3n R, Fdez-Riverola F. GC4S: a bioinformatics-oriented Java software library of reusable graphical user interface components. 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