{"id":1059,"date":"2016-07-27T10:34:17","date_gmt":"2016-07-27T10:34:17","guid":{"rendered":"http:\/\/www.virologyhighlights.com\/?p=1059"},"modified":"2018-05-25T08:31:47","modified_gmt":"2018-05-25T08:31:47","slug":"creating-phagonaute-a-web-based-interface-for-homology-search","status":"publish","type":"post","link":"https:\/\/www.elsevierblogs.com\/virology\/creating-phagonaute-a-web-based-interface-for-homology-search\/","title":{"rendered":"Creating ‘Phagonaute’ a web-based interface for homology searches"},"content":{"rendered":"

Read the full article on ScienceDirect.<\/a><\/h3>\n

Allowing phage synteny browsing and protein function prediction<\/h2>\n

Text by Marie-Agnes Petit<\/em><\/p>\n

The recent renewed interest for phages and viruses in general, has lead to the sequencing and tentative annotating of hundreds of new phage genomes. However, from this huge wave of new information the phage \u201cdark matter\u201d concept has also emerged, referring to the fact that the vast majority of phage genes resist annotation. Our earlier work, as well as the work of many others, had nevertheless suggested that part of the problem was due to unfit tools for homology search. Due to the remarkable divergence of phage proteins, simple BLAST searches are often unproductive. This paper describes the setting up of the \u201cPhagonaute\u201d web interface allowing the navigation among complete phage genomes, and taking into account this difficulty. Its purpose is to allow \u201cmodule\u201d comparisons across genomes, based on distant protein homologies. Within a window of 6-12 genes around a specific query gene, all homology relationships with related phages are displayed graphically, using a color code. Synteny conservation serves to strengthen the potential new function prediction uncovered by distant homology. This tool is therefore designed to help experimentalists to pick the right gene for the right experiment.<\/p>\n

The motivation to build up this site came from the fact that in the bacterial or eukaryotic world, such tools already exist and greatly help experimental research. One of the first websites serving this purpose was created by Ross Overbeek a long time ago and still serves today: it is entitled the \u2018show neighborhood\u2019 function, on the Integrated Microbial Genome (IMG) site of the Joint Genome Institute. Genomicus is its counterpart (with a different design) for Eukaryots.<\/p>\n

Before publishing this work, we used the site for our research purposes, mainly interrogating genes with functions related to homologous recombination, and were surprised by the amount of fruitful guesses it permitted (these are given in the paper as examples of use).<\/p>\n

The main problem we had to overcome was the treatment of protein fusions, which could easily meddle up the results. Let us say a query starts with a protein resulting from the fusion of an exonuclease with a recombinase, it will indistinctly display as \u2018homologs\u2019 many exonuclease and recombinase proteins which are distinct proteins. We solved this by splitting genes into \u2018domains\u2019 (which are not functional domains, but domains of homology). This gives to the output graphic an additional level of refinement, the mapping of the homology region.<\/p>\n

We hope this new phage tool will lead to many exciting discoveries and will contribute, with time, to decrease the phage dark matter.<\/p>\n

\"Petit_image\"<\/p>\n

Figure legend<\/strong><\/h3>\n
\n

Using co-occurrence to detect new functions. Starting from the hkaK<\/em> gene (in red) with unknown function, encoded by phage HK620 (infecting E. coli<\/em>), Phagonaute displays a large list of distant homologs, among which some are annotated as SSB (see legend). In addition, the sak4<\/em> gene (also named hkaL<\/em>, in green, right to hkaK<\/em> in HK620) is often co-occurrent with this putative ssb<\/em>.<\/p>\n

Introducing the author<\/strong><\/h3>\n

\"Picture1\"<\/p>\n

Marie-Agnes Petit<\/p>\n

<\/p>\n<\/div>\n

About the research<\/strong><\/h3>\n

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction<\/em><\/a>
\nVirology<\/em>, Volume 496, September 2016, Pages 42\u201350
\nHadrien Delattre, Oussema Souiai, Khema Fagoonee, Rapha\u00ebl Guerois, Marie-Agn\u00e8s Petit<\/p>\n","protected":false},"excerpt":{"rendered":"

Read the full article on ScienceDirect. Allowing phage synteny browsing and protein function prediction Text by Marie-Agnes Petit The recent renewed interest for phages and viruses in general, has lead to the sequencing and tentative annotating of hundreds of new phage genomes. However, from this huge wave of new information the phage \u201cdark matter\u201d concept Read More…<\/a><\/p>\n","protected":false},"author":1,"featured_media":1060,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,633],"tags":[799,800,803,794,798,802,801,796,792,795,797,790,791,793,804],"class_list":["post-1059","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-highlighted-article","category-virus-structure","tag-dark-matter","tag-database","tag-genomicus","tag-hadrien-delattre","tag-homology","tag-integrated-microbial-genome","tag-interface","tag-khema-fagoonee","tag-marie-agnes-petit","tag-oussema-souiai","tag-phage-tool","tag-phages","tag-phagonaute","tag-raphael-guerois","tag-synteny"],"_links":{"self":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/1059","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/comments?post=1059"}],"version-history":[{"count":5,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/1059\/revisions"}],"predecessor-version":[{"id":1074,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/1059\/revisions\/1074"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/media\/1060"}],"wp:attachment":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/media?parent=1059"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/categories?post=1059"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/tags?post=1059"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}