{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T21:07:28Z","timestamp":1770412048823,"version":"3.49.0"},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret \u2013 especially within overlapping genes; and viruses often employ non-canonical translational mechanisms \u2013 e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites \u2013 which can conceal potentially coding open reading frames (ORFs).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In a previous paper we introduced a new statistic \u2013 MLOGD (Maximum Likelihood Overlapping Gene Detector) \u2013 for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs \u2013 in particular overlapping or short CDSs \u2013 and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/guinevere.otago.ac.nz\/mlogd.html\" ext-link-type=\"uri\">http:\/\/guinevere.otago.ac.nz\/mlogd.html<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-7-75","type":"journal-article","created":{"date-parts":[[2006,2,17]],"date-time":"2006-02-17T07:48:35Z","timestamp":1140162515000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["Detecting overlapping coding sequences in virus genomes"],"prefix":"10.1186","volume":"7","author":[{"given":"Andrew E","family":"Firth","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris M","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,2,16]]},"reference":[{"key":"814_CR1","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1101\/gr.10.4.394","volume":"10","author":"GD Stormo","year":"2000","unstructured":"Stormo GD: Gene-finding approaches for eukaryotes. 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