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SIROCCO Releases Bioinformatics Tools for Data Analysis, Artificial miRNA Design

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Roughly two years after its was established by the European Commission, a consortium of researchers focused on RNA silencing has made publicly available a suite of bioinformatics tools developed by its members for analyzing the vast amounts of sequencing data generated by the initiative, as well as a web-based application for designing artificial miRNAs.

In doing so, SIROCCO — short for Silencing RNAs: Organizers and Coordinators of Complexity in Eukaryotic Organisms — has begun to meet its goal of making its discoveries and technologies freely accessible to the research community, according to SIROCCO project manager Aileen Hogan.

The kinds of tools now offered on the SIROCCO site are available elsewhere, such as within the National Institute's of Health's Gene Expression Omnibus, but tracking them down can be difficult and time consuming, she noted.

"We are going to try to simplify it all to make [these kinds of resources] more accessible to everyone … so that [the portal becomes] a sort of one-stop shop for people doing [small RNA] analysis, even if they're not in the consortium," Hogan said.

The bioinformatics portal is also expected to help consortium members makes sense of the data their projects have been generating since SIROCCO was launched in 2007 with €11.8 million ($15.1 million) in EC funding (see RNAi News, 4/26/2007).

"Because more and more of the participants in this consortium do high-throughput sequencing, [the bioinformatics tools represent] a way to manage those big datasets as they come off the … sequencers," Hogan said. "They come off in very big files, and a lot of people … are at a bit of a loss [when it comes to] how to analyze that stuff. Hopefully, these tools that the consortium is coming up with are going to help."

And while existing SIROCCO participants have thus far been responsible for developing the tools, Hogan said that the consortium is now planning to seek a new member with bioinformatics expertise to oversee such activities.

"We had a talk at our annual meeting in December about … what new partner is needed," she said. Although many of the groups in SIROCCO have bioinformatics specialists in-house, "they thought a dedicated one would be good."

Hogan said that the search for the new member would officially kick off in about three months.

The Tools

SIROCCO was established to "characterize the full complement" of miRNAs and siRNAs in animals and plants using bioinformatics, genomics, biochemistry, cell biology, and genetics to "reveal how these RNAs are produced and processed, how they are transported, and how they target specific genes and RNAs for silencing," according to the organization.

Consortium members are also investigating the roles of miRNA and siRNA in disease development and differentiation, and how small RNAs help to regulate networks and interact with other cellular-control mechanisms.

As part of that effort, SIROCCO members have created a number of web-based applications to help streamline the organization's various projects, including the University of East Anglia's Plant Small RNA Toolkit.

Among the tools available in this resource is a sequence file pre-processing tool; a tool for filtering sequences in large-scale data sets; an application for generating an expression profile of known miRNAs in large-scale small RNA-sequencing experiments; a tool for identifying miRNAs in high-throughput sequence data; and a tool for predicting plant miRNA targets.

The bioinformatics portal also includes WMD2, a web-based tool for the automated design of artificial miRNAs, and SHORE, a mapping and analysis pipeline for Illumina Genome Analyzer expression data, including those from mRNA-sequencing and small RNA-sequencing experiments. Also available is At-TAX, which is a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana.

These three tools were developed at the Max Planck Institute for Developmental Biology.

Replacing Rosetta

In late 2007, RNAi News reported that SIROCCO was on the lookout for a new member or members to replace Rosetta Genomics, which had initially agreed to join the organization but later withdrew for what SIROCCO called "reasons related to contract administration" (see RNAi News, 11/20/2007).

According to Hogan, replacements were found in CEINGE-Biotecnologie Avanzate, an Italian non-profit consortium focused on developing biotechnologies for healthcare applications; and InteRNA Technologies, a Dutch developer of miRNA diagnostics and therapeutics.

Specifically, CEINGE is investigating the role of miRNAs in stem-cell biology, while InteRNA is focusing on miRNAs and cancer, Hogan said.

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