miRanalyser is a free web-server tool for the processing of small-RNAs data obtained from next generation sequencing techniques such as the Genome Analyzer of Illumina Inc. or Genome SequencerTM FLX (454 Life ScienceTM and Roche Applied Science). The input data are grouped sequence reads (sequence tags, unique reads) that are typically 16 to 26 bp long (depending on the sequencing protocol), and their expression values (number of times the unique read has been found to be expressed in the experiment). Then, the tool performs several analysis steps and outputs detailed results. The analysis steps are the following:
- Alignment of all reads against the libraries of known mature microRNAs (including also the mature-star libraries – the sequences which pair with the mature microRNAs in the secondary structure of the pre-microRNAs). Additionally, the tool outputs the predicted target genes together with direct links to ontological analyses of the predictions.
- Mapping against all theoretically possible mature-star microRNAs including those which are not annotated in miRBase. This allows to detect the expression of previously undetected mature-star microRNAs.
- Alignment against other libraries of transcribed sequences. For example, the number of matches found in the transcriptome will be inversely proportional to the RNA sample quality (the fewer degradation products, the fewer the matches). Furthermore, matches found in RFam will indicate expression of other small ncRNA molecules.
- Prediction of previously unknown microRNAs. This is important as 1) experiments can be mined for the detection of previously unknown microRNAs and 2) for many species none or just a few microRNAs are known and therefore the detection of microRNAs relies almost entirely on the computational prediction of new microRNAs
Tutorial and more information at: http://web.bioinformatics.cicbiogune.es/microRNA/manual.html