The SIROCCO consortium welcomes three new partners selected by competitive call who will participate for the remainder of the project
Anton Enright at the EBI and Jaak Vilo at Quretec are developing computational methods for the analysis of sRNA datasets produced in the consortium, as well as improved data submission and management tools.
Markus Stoffel at ETHZ is developing technologies to substitute, overexpress or silence sRNAs in vivo using knockout mouse models.
A toolkit for analyzing large-scale animal small RNA datasets.
Tools available include
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 many of the tools used in the bioinformatic sphere.
Sirocco have today released A FASTA Maker – a Java based tool to help perform these SOFT to FASTA file conversions in an easy to use GUI.
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.
Click here to read more about and use the A FASTA Maker tool.
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The session will be chaired by Gunter Meister (Martinsried), and the speakers will be Thomas Meyer (Berlin), Jørgen Kjems (Aarhus) and Eric Miska (Cambridge).
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.
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.
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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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.
SIROCCO Coordinator David Baulcombe receives knighthood for services to plant sciences. Read more here
SIROCCO Partner Detlef Weigel elected to US National Academy of Sciences as a Full Member