Computational analysis of small RNA cloning data

作者: Philipp Berninger , Dimos Gaidatzis , Erik van Nimwegen , Mihaela Zavolan

DOI: 10.1016/J.YMETH.2007.10.002

关键词: Computational biologymicroRNABiologyGeneticsComputational analysisSmall RNAOligonucleotide MicroarrayAnnotationDeep sequencingFast algorithmGene expression profilingGeneral Biochemistry, Genetics and Molecular BiologyMolecular biology

摘要: Cloning and sequencing is the method of choice for small regulatory RNA identification. Using deep technologies one can now obtain up to a billion nucleotides--and tens millions RNAs--from single library. Careful computational analyses such libraries enabled discovery miRNAs, rasiRNAs, piRNAs, 21U RNAs. Given large number sequences that be obtained from each individual sample, may soon become an alternative oligonucleotide microarray technology mRNA expression profiling. In this report we present methods developed annotation profiling RNAs through large-scale sequencing. These include fast algorithm finding nearly perfect matches in sequence databases, web-accessible software system libraries, Bayesian comparing across samples.

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