2012).Īlmost all small RNAs derive from post-transcriptional processing of larger RNA precursors. Deeply sequenced small RNA libraries allow experimental discovery of expressed small RNAs, as well as quantification based upon read-counts (although the latter can be subject to biases inherent to RNA ligation, adapter sequences and amplification) ( Jayaprakash et al. Typical small RNA-seq experiments use RNA ligase to attach adapters to the 3′ and 5′ ends of size-fractionated total RNAs, followed by reverse-transcription, PCR amplification, and shotgun sequencing of the resulting cDNA library. Small RNA sequencing (small RNA-seq), enabled by modern highly parallel DNA sequencing instruments, is a powerful method for discovery, annotation, and quantification of small RNA-producing genes. Small RNAs are ubiquitous regulatory molecules produced by many thousands of endogenous genes. ShortStack is freely available under a GNU General Public License. Annotation of MIRNA loci by ShortStack is highly specific in both plants and animals. ShortStack efficiently processes very large small RNA-seq data sets using modest computational resources, and its performance compares favorably to previously described tools. In this study, ShortStack is demonstrated to perform accurate annotations and useful descriptions of diverse small RNA genes from four plants ( Arabidopsis, tomato, rice, and maize) and three animals ( Drosophila, mice, and humans). ShortStack’s output reports multiple parameters of direct relevance to small RNA gene annotation, including RNA size distributions, repetitiveness, strandedness, hairpin-association, MIRNA annotation, and phasing. ShortStack is a stand-alone application that analyzes reference-aligned small RNA-seq data and performs comprehensive de novo annotation and quantification of the inferred small RNA genes. However, in many organisms and tissue types, MIRNA genes comprise only a small fraction of all small RNA-producing genes. Many tools have been described for annotation and quantification of microRNA loci ( MIRNAs) from small RNA-seq data. Small RNA sequencing allows genome-wide discovery, categorization, and quantification of genes producing regulatory small RNAs.
0 kommentar(er)
