Computational analysis of small RNA cloning data

@article{citeulike:2187167, 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.}, author = {Berninger, Philipp and Gaidatzis, Dimos and van Nimwegen, Erik and Zavolan, Mihaela }, booktitle = {MicroRNAs: Part B}, citeulike-article-id = {2187167}, doi = {http://dx.doi.org/10.1016/j.ymeth.2007.10.002}, journal = {Methods}, keywords = {bayesian, cloning, expression, methods, mirna, quantitation}, month = {January}, number = {1}, pages = {13--21}, posted-at = {2008-07-08 19:01:01}, priority = {2}, title = {Computational analysis of small RNA cloning data}, url = {http://dx.doi.org/10.1016/j.ymeth.2007.10.002}, volume = {44}, year = {2008} }

TY - JOUR ID - citeulike:2187167 L3 - citeulike-article-id:2187167 TI - Computational analysis of small RNA cloning data T2 - MicroRNAs: Part B JF - Methods VL - 44 IS - 1 SP - 13 EP - 21 N2 - 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. KW - bayesian KW - cloning KW - expression KW - methods KW - mirna KW - quantitation AU - Berninger, Philipp AU - Gaidatzis, Dimos AU - van Nimwegen, Erik AU - Zavolan, Mihaela PY - 2008/01// UR - http://dx.doi.org/10.1016/j.ymeth.2007.10.002 ER -