{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T10:23:13Z","timestamp":1758709393873},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: AGO(Argonaute)-binding domains, composed of repeated motifs, in which only binary combinations of tryptophan and glycine are conserved, bind AGO proteins and are essential during RNAi-mediated gene silencing. The amino acid sequence of this domain is extremely divergent and therefore very difficult to detect. Commonly used bioinformatic tools fail to identify tryptophan\u2013glycine and\/or glycine\u2013tryptophan motifs (WG\/GW) domains and currently there is no publicly available software which can detect these weakly conserved, but functional AGO-binding segments.<\/jats:p>\n               <jats:p>Results: Recently, we have developed an algorithm based on compositional analysis of the amino acid content of the domain. We have demonstrated that the algorithm can be successfully applied for the identification of the new WG\/GW proteins in the Arabidopsis genome. Here we introduce Agos (Argonaute-binding domain screener), a novel universal web service for de novo identification of WG\/GW domains in protein sequences. The web implementation of the algorithm contains several new features and enhancements: (i) one universal scoring matrix which allows identification of AGO-binding proteins in sequences representing all organisms; (ii) reduction of false positive predictions by improved selectivity of the algorithm; (iii) graphical interface to easily browse the prediction results; and (iv) the option to submit a DNA sequence which will be automatically translated in six frames before running the prediction algorithm.<\/jats:p>\n               <jats:p>Availability: Freely available at: http:\/\/bioinfo.amu.edu.pl\/agos\/.<\/jats:p>\n               <jats:p>Contact: \u00a0wmk@amu.edu.pl<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr128","type":"journal-article","created":{"date-parts":[[2011,3,9]],"date-time":"2011-03-09T01:45:56Z","timestamp":1299635156000},"page":"1318-1319","source":"Crossref","is-referenced-by-count":11,"title":["Agos\u2014a universal web tool for GW Argonaute-binding domain prediction"],"prefix":"10.1093","volume":"27","author":[{"given":"Andrzej","family":"Zielezinski","sequence":"first","affiliation":[{"name":"Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wojciech M.","family":"Karlowski","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Genomics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,8]]},"reference":[{"key":"2023012512190783700_B1","doi-asserted-by":"crossref","first-page":"5020","DOI":"10.1128\/MCB.00076-09","article-title":"Two GW repeat proteins interact with Tetrahymena thermophila argonaute and promote genome rearrangement","volume":"29","author":"Bednenko","year":"2009","journal-title":"Mol. Cell. Biol."},{"key":"2023012512190783700_B2","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/embor.2009.31","article-title":"RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family","volume":"10","author":"Bies-Etheve","year":"2009","journal-title":"EMBO Rep."},{"key":"2023012512190783700_B3","doi-asserted-by":"crossref","first-page":"2539","DOI":"10.1101\/gad.451207","article-title":"Reiterated WG\/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components","volume":"21","author":"El-Shami","year":"2007","journal-title":"Genes Dev."},{"key":"2023012512190783700_B4","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1261\/rna.1703809","article-title":"The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing","volume":"15","author":"Eulalio","year":"2009","journal-title":"RNA"},{"key":"2023012512190783700_B5","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.cell.2009.04.028","article-title":"An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein","volume":"137","author":"He","year":"2009","journal-title":"Cell"},{"key":"2023012512190783700_B6","doi-asserted-by":"crossref","first-page":"4231","DOI":"10.1093\/nar\/gkq162","article-title":"Genome-wide computational identification of WG\/GW Argonaute-binding proteins in Arabidopsis","volume":"38","author":"Karlowski","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1318\/48869631\/bioinformatics_27_9_1318.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1318\/48869631\/bioinformatics_27_9_1318.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:14:17Z","timestamp":1674659657000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/9\/1318\/242874"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,8]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2011,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr128","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,5,1]]},"published":{"date-parts":[[2011,3,8]]}}}