A toolkit for analysing large-scale plant small RNA datasets.

Bioinformatics
Simon MoxonVincent Moulton

Abstract

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. The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk.

References

Apr 6, 2005·Developmental Cell·Rebecca SchwabDetlef Weigel
Apr 27, 2005·Cell·Edwards AllenJames C Carrington
May 6, 2005·Functional & Integrative Genomics·Anthony A Millar, Peter M Waterhouse
Mar 29, 2006·Trends in Genetics : TIG·Peter Brodersen, Olivier Voinnet
May 4, 2006·Annual Review of Plant Biology·Matthew W Jones-RhoadesBonnie Bartel
Nov 4, 2006·Cell·Michael J AxtellDavid P Bartel
Dec 22, 2006·Genes & Development·Ramya RajagopalanDavid P Bartel
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ho-Ming ChenShu-Hsing Wu
Nov 15, 2007·Nucleic Acids Research·Tyler W H BackmanKristin D Kasschau
Dec 26, 2007·Methods : a Companion to Methods in Enzymology·Markus HafnerThomas Tuschl
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rebecca A MosherDavid C Baulcombe
Apr 9, 2008·Nature Biotechnology·Marc R FriedländerNikolaus Rajewsky
May 10, 2008·Bioinformatics·Kay PrüferJanet Kelso

❮ Previous
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Citations

Dec 17, 2009·Planta·Inês TrindadeDulce Metelo Dos Santos
Aug 30, 2011·Plant Molecular Biology·Guiling Sun
Feb 1, 2012·Plant Molecular Biology·Fuliang XieBaohong Zhang
Mar 10, 2012·Plant Molecular Biology·Hua PengSheng-hua Wang
Mar 22, 2012·Omics : a Journal of Integrative Biology·Antonio Muñoz-MéridaAntonio J Pérez-Pulido
Jul 31, 2009·Briefings in Functional Genomics & Proteomics·Frank SchwachTamas Dalmay
Dec 21, 2011·Briefings in Functional Genomics·David J Studholme
Apr 1, 2009·Briefings in Bioinformatics·Chad J CreightonPreethi H Gunaratne
Oct 30, 2009·Briefings in Bioinformatics·David Stephen HornerGraziano Pesole
Jan 26, 2011·Briefings in Bioinformatics·Yijun MengMing Chen
Jul 20, 2012·Briefings in Bioinformatics·Chaogang ShaoYijun Meng
Aug 31, 2010·Bioinformatics·Roy RonenNoam Shomron
Sep 8, 2011·Bioinformatics·Wenming ZhaoSongnian Hu
Dec 16, 2011·Bioinformatics·Antonio Marco, Sam Griffiths-Jones
Dec 16, 2011·Bioinformatics·Thomas J HardcastleDavid C Baulcombe
Aug 24, 2012·Bioinformatics·Vikas GuptaStig U Andersen
Dec 22, 2010·Journal of Experimental Botany·G Le TrionnaireD Twell
Mar 2, 2011·Journal of Experimental Botany·Filipe BorgesJörg D Becker
May 19, 2010·Nucleic Acids Research·Erle ZhuJinyu Wu
Dec 12, 2012·Nucleic Acids Research·Jiyuan AnColleen C Nelson
Mar 13, 2012·The Plant Cell·Padubidri V ShivaprasadDavid C Baulcombe
Feb 20, 2010·BMC Bioinformatics·Daniel MacLeanDavid J Studholme
Dec 22, 2009·BMC Genomics·Daniel KlevebringStefan Jansson
Jan 1, 2010·BMC Genomics·Robert Grant-DowntonHugh Dickinson
Feb 18, 2011·BMC Genomics·Vivek ThakurXin-Guang Zhu
Jul 4, 2012·BMC Genomics·Flávia ThiebautPaulo Cavalcanti Gomes Ferreira
Jan 11, 2013·BMC Genomics·Somrak NumnarkDuangdao Wichadakul

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