Literature DB >> 18713789

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

Simon Moxon1, Frank Schwach, Tamas Dalmay, Dan Maclean, David J Studholme, Vincent Moulton.   

Abstract

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

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Year:  2008        PMID： 18713789     DOI： 10.1093/bioinformatics/btn428

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  133 in total

1.  A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs.

Authors:  Padubidri V Shivaprasad; Ho-Ming Chen; Kanu Patel; Donna M Bond; Bruno A C M Santos; David C Baulcombe
Journal:  Plant Cell       Date:  2012-03-09       Impact factor: 11.277

2.  MicroRNA profiles and their control of male gametophyte development in rice.

Authors:  Hua Peng; Jun Chun; Tao-bo Ai; Yong-ao Tong; Rong Zhang; Ming-ming Zhao; Fang Chen; Sheng-hua Wang
Journal:  Plant Mol Biol       Date:  2012-03-09       Impact factor: 4.076

3.  Identification of miRNAs in sorghum by using bioinformatics approach.

Authors:  Amit Katiyar; Shuchi Smita; Viswanathan Chinnusamy; Dev Mani Pandey; Kailash Bansal
Journal:  Plant Signal Behav       Date:  2012-02-01

4.  High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.

Authors:  Natalie W Breakfield; David L Corcoran; Jalean J Petricka; Jeffrey Shen; Juthamas Sae-Seaw; Ignacio Rubio-Somoza; Detlef Weigel; Uwe Ohler; Philip N Benfey
Journal:  Genome Res       Date:  2011-09-22       Impact factor: 9.043

Review 5.  Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.

Authors:  Molly Megraw; Jason S Cumbie; Maria G Ivanchenko; Sergei A Filichkin
Journal:  Plant Cell       Date:  2016-02-11       Impact factor: 11.277

Review 6.  Expression profiling of microRNAs by deep sequencing.

Authors:  Chad J Creighton; Jeffrey G Reid; Preethi H Gunaratne
Journal:  Brief Bioinform       Date:  2009-03-30       Impact factor: 11.622

7.  CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

Authors:  Irina Mohorianu; Matthew Benedict Stocks; John Wood; Tamas Dalmay; Vincent Moulton
Journal:  RNA Biol       Date:  2013-06-28       Impact factor: 4.652

8.  High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans).

Authors:  Weihua Liu; Chunzhen Cheng; Fanglan Chen; Shanshan Ni; Yuling Lin; Zhongxiong Lai
Journal:  BMC Plant Biol       Date:  2018-11-29       Impact factor: 4.215

9.  miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula.

Authors:  Inês Trindade; Cláudio Capitão; Tamas Dalmay; Manuel Pedro Fevereiro; Dulce Metelo Dos Santos
Journal:  Planta       Date:  2009-12-11       Impact factor: 4.116

10.  Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs.

Authors:  Kashmir Singh; Aarthi Talla; Wenping Qiu
Journal:  Funct Integr Genomics       Date:  2012-08-19       Impact factor: 3.410
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