{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T12:32:24Z","timestamp":1779193944225,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T00:00:00Z","timestamp":1724889600000},"content-version":"vor","delay-in-days":241,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["101041421"],"award-info":[{"award-number":["101041421"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Visualization and comparison of genome maps of bacteriophages can be very effective, but none of the tools available on the market allow visualization of gene conservation between multiple sequences at a glance. In addition, most bioinformatic tools running locally are command line only, making them hard to setup, debug, and monitor.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To address these motivations, we developed synphage, an easy-to-use and intuitive tool to generate synteny diagrams from GenBank files. This software has a user-friendly interface and uses metadata to monitor the progress and success of the data transformation process. The output plot features colour-coded genes according to their degree of conservation among the group of displayed sequences. The strength of synphage lies also in its modularity and the ability to generate multiple plots with different configurations without having to re-process all the data. In conclusion, synphage reduces the bioinformatic workload of users and allows them to focus on analysis, the most impactful area of their work.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The synphage tool is implemented in the Python language and is available from the GitHub repository at https:\/\/github.com\/vestalisvirginis\/synphage. This software is released under an Apache-2.0 licence. A PyPI synphage package is available at https:\/\/pypi.org\/project\/synphage\/ and a containerized version is available at https:\/\/hub.docker.com\/r\/vestalisvirginis\/synphage. Contributions to the software are welcome whether it is reporting a bug or proposing new features and the contribution guidelines are available at https:\/\/github.com\/vestalisvirginis\/synphage\/blob\/main\/CONTRIBUTING.md.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioadv\/vbae126","type":"journal-article","created":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T22:10:49Z","timestamp":1724969449000},"source":"Crossref","is-referenced-by-count":3,"title":["synphage: a pipeline for phage genome synteny graphics focused on gene conservation"],"prefix":"10.1093","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8249-7182","authenticated-orcid":false,"given":"Virginie","family":"Grosboillot","sequence":"first","affiliation":[{"name":"Department of Microbiology, Biotechnical Faculty, University of Ljubljana , 1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Dragos\u030c","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Biotechnical Faculty, University of Ljubljana , 1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,8,29]]},"reference":[{"key":"2024090221345404100_vbae126-B1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1145\/360262.360268","article-title":"Biopython: Python tools for computational biology","volume":"20","author":"Chapman","year":"2000","journal-title":"SIGBIO Newsl"},{"key":"2024090221345404100_vbae126-B2","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and 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