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SIROCCO Tools

Here is a list of tools which can be used to process data for silencing RNA. Unsure how to proceed? Try our getting started guide.

UEA Animal Small RNA Toolkit

A toolkit for analyzing large-scale animal small RNA datasets.

Click here to visit the site.

Tools available include

  • Sequence file pre-processing: Sequence adaptor removal and conversion to FASTA format
  • Filter tool: Filter sequences in large-scale data sets
  • miRProf: Expression profiles of known miRNAs from large scale sRNA data sets
  • miRCat: Identification of miRNA sequences in large-scale sRNA data sets
  • SiLoCo: Identification and comparison of sRNA-producing loci in large-scale data sets
  • SiLoMa: Generate graphical maps of individual sRNA loci.
  • RNA folding/annotation: For highlighting sRNA locations on a folded RNA sequence.

A FASTA Maker – SOFT to FASTA file conversion utility

Many toolkits (for example the UEA Small Plant and Animal toolkit) require data to be provided in FASTA format. However sequence data sets from GEO often come in the SOFT format, and hence need to be converted before they can be used by the many tools used in the bioinformatic sphere.

This utility operates in two modes – it can either transform local SOFT files containing sequence data into FASTA data or, given an accession number, can fetch a dataset from GEO. It also allows the creation of a ZIP version of the newly created FASTA file and a choice or redundant or non-redundant FASTA formats.

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Seqbuster offers analysis of deep sequencing data

SeqBuster is a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs.SeqBuster includes a stand-alone version that permits the annotation against any custom database installed in the local machine independently of the web server tool. This offers a pre-analysis that is not restricted to the databases stored in the web server, overcoming the limitations in the storage capacities detected in other web-based bioinformatic tools. The R environment in which the different analysis packages have been developed permits the incorporation and/or modification of different types of analysis, which may be focused not only on small non-coding RNAs, but also on any type of sequence generated in large-scale sequencing strategies. SeqBuster is highly versatile offering a wide range of options both in the pre-analysis for annotation purposes and in the different module analysis for data manipulation.

Click here to access the tool.

SeqBuster is developed by the Genes and Diseases Group at the Centre for Genomic Regulation (Sirocco Partner 14). It has been developed and was presented to the Sirocco at the Sirocco Conference in 2009.

Sirocco Animitap: MicroRNA Target Prediction Tool

The Sirocco Animitap microRNA Target Prediction Aggregator website has been developed to allow the comparison of results from a number of microRNA target prediction tools, and/or the same algorithm in parallel with varying parameters to compare outputs. The Animitap system has been launched with the ability to run Miranda and RNAHybrid, with others to follow. These programs have been compiled from provided sources. Each algorithm is presented to the user in a basic mode for default options (to assist the novice user), or with a full set of command line features made available to the user. The users data is uploaded in FASTA format and then queued to run on the server. After each algorithm has run to completion the Animitap system sends an email to the user with a link where the user can download the results file with a copy of the program command line for archiving purposes and/or an error log if appropriate.

You can view the Target Prediction tool here.

The Sirocco Pipeline – A Bioinformatics Service for SIROCCO Members

A SIROCCO pipeline has been developed for analysing the results of high throughput sequencing experiments. It is currently used most often for Illumina reads but can be used to process 454 reads as well.
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Files for cloning workshop, bioinformatics session (Col0 seedling)

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WMD3 – Web MicroRNA Designer

WMD (Web MicroRNA Designer) is a web-tool for the automated design of artificial microRNAs. Version 3 was released in July 2009.
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UEA Plant Small RNA Toolkit

A toolkit for analyzing large-scale plant small RNA datasets.
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baySeq Differential Analysis Tool

baySeq is a package for calculating Differential Expression in Solexa-type, or count, data for the R Project For Statistical Computing. It was previously available on these pages but is now part of Bioconductor. For more information please see the Bioconductor website.

For details on the methods being used, consult Hardcastle et al. (2009) Empirical Bayesian methods for estimating differential expression in count data.

Arabidopsis thaliana – Tiling Array Express (At-TAX)

At-TAX is a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Tiling array hybridization intensities, probe set definitions for Arabidopsis genes and segmentations into exonic and background regions are visualized in a genome browser. Visualizations of gene expression and cross-platform comparisons are available through tileViz.
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