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

UEAsRNA

:: 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

 NO

:: 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.

CPSS 1.1 – Computational Platform for analysis of Small RNA Deep Sequencing data

CPSS 1.1

:: DESCRIPTION

CPSS is a web server which provides a comprehensively and systemically integrated pipeline for analyzing small RNA deep sequencing data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CPSS: a computational platform for the analysis of small RNA deep sequencing data.
Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, Cooke HJ, Xue Y, Shi Q.
Bioinformatics. 2012 Jul 15;28(14):1925-7. doi: 10.1093/bioinformatics/bts282

sPARTA 1.12 – small RNA-PARE Target Analyzer

sPARTA 1.12

:: DESCRIPTION

sPARTA is a high performance software for the validation of plant miRNA or sRNA targets with PARE (Parallel Analysis of Read Ends) data.

miRferno is a target prediction module of sPARTA with standard and seed-free prediction modes.

::DEVELOPER

the Meyers lab at the University of Delaware.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sPARTAmiRferno

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct;42(18):e139. doi: 10.1093/nar/gku693. Epub 2014 Aug 12.
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC

segmentSeq 2.2.2 – Identifying small RNA loci from High-throughput Sequencing data

segmentSeq 2.2.2

:: DESCRIPTION

segmentSeq is a methods for identifying small RNA loci from high-throughput sequencing data

::DEVELOPER

Thomas J. Hardcastle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 segmentSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.
Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.

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

Oasis 1.0 – small RNA Classification

Oasis 1.0

:: DESCRIPTION

Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data.

::DEVELOPER

Oasis team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Java

:: DOWNLOAD

 Oasis

:: MORE INFORMATION

Citation:

Oasis: online analysis of small RNA deep sequencing data.
Capece V, Vizcaino JC, Vidal R, Rahman RU, Centeno TP, Shomroni O, Suberviola I, Fischer A, Bonn S.
Bioinformatics. 2015 Feb 19. pii: btv113.