sRNAtoolbox 1.3.1 – Collection of small RNA Analysis tools

sRNAtoolbox 1.3.1

:: DESCRIPTION

sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools.The center piece of sRNAtoolbox is sRNAbench, which allows for expression profiling from deep sequencing experiments.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser / Linux

:: DOWNLOAD

sRNAtoolBox

:: MORE INFORMATION

Citation

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.
Aparicio-Puerta E, Lebrón R, Rueda A, Gómez-Martín C, Giannoukakos S, Jaspez D, Medina JM, Zubkovic A, Jurak I, Fromm B, Marchal JA, Oliver J, Hackenberg M.
Nucleic Acids Res. 2019 Jul 2;47(W1):W530-W535. doi: 10.1093/nar/gkz415.

Nucleic Acids Res. 2015 May 27. pii: gkv555.
sRNAtoolbox: an integrated collection of small RNA research tools.
Rueda A, Barturen G, Lebrón R, Gómez-Martín C, Alganza á, Oliver JL, Hackenberg M

UEA sRNA Workbench 4.6 ALPHA – Analysing micro RNA and other small RNA data from High-Throughput Sequencing devices

UEA sRNA Workbench 4.6 ALPHA

:: DESCRIPTION

The UEA sRNA workbench is a new simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample sRNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data.

::DEVELOPER

the RNA Computational Biology group at the University of East Anglia (UEA)

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux /MacOsX
Java

:: DOWNLOAD

UEA sRNA Workbench

:: MORE INFORMATION

Citation

Stocks, M. B.; Moxon, S.; Mapleson, D.; Woolfenden, H. C.; Mohorianu, I.; Folkes, L.; Schwach, F.; Dalmay, T. & Moulton, V. (2012)
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets.
Bioinformatics ,Vol. 28,pp. 2059-2061

RNA Biol. 2013 Jul;10(7):1221-30. doi: 10.4161/rna.25538. Epub 2013 Jun 28.
CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.
Mohorianu I1, Stocks MB, Wood J, Dalmay T, Moulton V.

Chimira 1.5 – Analysis of small RNA Sequencing data and microRNA modifications

Chimira 1.5

:: DESCRIPTION

Chimira is an online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile.

::DEVELOPER

Chimira team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Chimira: Analysis of small RNA Sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics. 2015 Jun 20. pii: btv380.

SeqBuster 3.5 – small RNA analysis of deep Sequencing data

SeqBuster 3.5

:: DESCRIPTION

SeqBuster is a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets.

::DEVELOPER

Estivill’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/ Windows
Java
mysql
R package

:: DOWNLOAD

SeqBuster

:: MORE INFORMATION

Citation

Specific Small-RNA Signatures in the Amygdala at Premotor and Motor Stages of Parkinson’s Disease Revealed by Deep Sequencing Analysis.
Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.
Pantano L, Estivill X, Martí E.
Nucleic Acids Res. 2010 Mar;38(5):e34. doi: 10.1093/nar/gkp1127.

Targetfinder 1.7 – Predict Small RNA Targets in a Sequence Database

Targetfinder 1.7

:: DESCRIPTION

Targetfinder predicts small RNA targets in a sequence database using a plant-based scoring metric.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl

:: DOWNLOAD

Targetfinder

:: MORE INFORMATION

Citation:

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. (2007)
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
PLoS ONE 2, e219.

P-SAMS – the Plant Small RNA Maker Suite

P-SAMS

:: DESCRIPTION

P-SAMS is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Perl
C++ Compiler

:: DOWNLOAD

P-SAMS

:: MORE INFORMATION

Citation:

P-SAMS: a web suite for plant artificial microRNA and synthetic trans-acting small interfering RNA design.
Fahlgren N, Hill ST, Carrington JC, Carbonell A.
Bioinformatics. 2015 Sep 17. pii: btv534

MicroRazerS 1.0 – Rapid Alignment of small RNA reads

MicroRazerS 1.0

:: DESCRIPTION

MicroRazerS is a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

::DEVELOPER

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MicroRazerS

:: MORE INFORMATION

Citation

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling.
MicroRazerS: rapid alignment of small RNA reads.
Bioinformatics (2010) 26 (1): 123-124

Ebbie-MM 4.3 – Analyze Single Mismatches of Small RNAs to the genome

Ebbie-MM 4.3

:: DESCRIPTION

Ebbie-MM (Ebbie-(mis)match) is a software that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications.

::DEVELOPER

H Alexander Ebhardt , Herbert H. Tsang and Denny C. Dai .

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Java
NCBI-Blast

:: DOWNLOAD

Ebbie-MM

:: MORE INFORMATION

Citation

H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bosta3 and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucl. Acids Res. (2009) 37 (8): 2461-2470