{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T02:28:51Z","timestamp":1768703331355,"version":"3.49.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci.<\/jats:p>\n               <jats:p>Availability: The tools are freely available for use at http:\/\/srna-tools.cmp.uea.ac.uk<\/jats:p>\n               <jats:p>Contact: \u00a0vincent.moulton@cmp.uea.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn428","type":"journal-article","created":{"date-parts":[[2008,8,20]],"date-time":"2008-08-20T02:49:03Z","timestamp":1219200543000},"page":"2252-2253","source":"Crossref","is-referenced-by-count":234,"title":["A toolkit for analysing large-scale plant small RNA datasets"],"prefix":"10.1093","volume":"24","author":[{"given":"Simon","family":"Moxon","sequence":"first","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]},{"given":"Frank","family":"Schwach","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]},{"given":"Tamas","family":"Dalmay","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]},{"given":"Dan","family":"MacLean","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]},{"given":"David J.","family":"Studholme","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]},{"given":"Vincent","family":"Moulton","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK"}]}],"member":"286","published-online":{"date-parts":[[2008,8,19]]},"reference":[{"key":"2023020211251415700_B1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.cell.2005.04.004","article-title":"microRNA-directed phasing during transacting siRNA biogenesis in plants","volume":"121","author":"Allen","year":"2005","journal-title":"Cell"},{"key":"2023020211251415700_B2","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.cell.2006.09.032","article-title":"A two-hit trigger for siRNA biogenesis in plants","volume":"127","author":"Axtell","year":"2006","journal-title":"Cell"},{"key":"2023020211251415700_B3","doi-asserted-by":"crossref","first-page":"D982","DOI":"10.1093\/nar\/gkm997","article-title":"Update of ASRP: the Arabidopsis small RNA project database","volume":"36","author":"Backman","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020211251415700_B4","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.tig.2006.03.003","article-title":"The diversity of RNA silencing pathways in plants","volume":"22","author":"Brodersen","year":"2006","journal-title":"Trends Genet"},{"key":"2023020211251415700_B5","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1093\/bioinformatics\/bth374","article-title":"Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences","volume":"20","author":"Bonnet","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020211251415700_B6","doi-asserted-by":"crossref","first-page":"3318","DOI":"10.1073\/pnas.0611119104","article-title":"Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis","volume":"104","author":"Chen","year":"2007","journal-title":"Proc. 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