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Computational analysis of small RNA cloning data

Berninger, P. and Gaidatzis, D. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of small RNA cloning data. Methods, Vol. 44, no. 1. S. 13-21.

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Official URL: http://edoc.unibas.ch/dok/A5259652

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Abstract

Cloning and sequencing is the method of choice for small regulatory RNA identification. Using deep sequencing technologies one can now obtain up to a billion nucleotides--and tens of millions of small RNAs--from a single library. Careful computational analyses of such libraries enabled the discovery of miRNAs, rasiRNAs, piRNAs, and 21U RNAs. Given the large number of sequences that can be obtained from each individual sample, deep sequencing may soon become an alternative to oligonucleotide microarray technology for mRNA expression profiling. In this report we present the methods that we developed for the annotation and expression profiling of small RNAs obtained through large-scale sequencing. These include a fast algorithm for finding nearly perfect matches of small RNAs in sequence databases, a web-accessible software system for the annotation of small RNA libraries, and a Bayesian method for comparing small RNA expression across samples.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)
UniBasel Contributors:van Nimwegen, Erik and Zavolan, Mihaela
Item Type:Article, refereed
Bibsysno:Link to catalogue
Publisher:Academic Press
ISSN:1046-2023
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:14 Sep 2012 06:50
Deposited On:22 Mar 2012 14:13

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