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BWA

Submitted by ChenLiang on Thu, 04/06/2017 - 17:10

The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently.

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RNAstructure

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

There are numerous examples of RNA-RNA complexes, including microRNA-mRNA and small RNA-mRNA duplexes for regulation of translation, guide RNA interactions with target RNA for post-transcriptional modification and small nuclear RNA duplexes for splicing. Predicting the base pairs formed between two interacting sequences remains difficult, at least in part because of the competition between unimolecular and bimolecular structure.

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RNAplex

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search.

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MIReNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are a class of endogenes derived from a precursor (pre-miRNA) and involved in post-transcriptional regulation. Experimental identification of novel miRNAs is difficult because they are often transcribed under specific conditions and cell types. Several computational methods were developed to detect new miRNAs starting from known ones or from deep sequencing data, and to validate their pre-miRNAs.

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NPInter

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between noncoding RNAs (ncRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs).

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miPred

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

To distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs), a hybrid feature which consists of local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure and P-value of randomization test is used. Besides, a novel machine-learning algorithm, random forest (RF), is introduced. The results suggest that our method predicts at 98.21% specificity and 95.09% sensitivity.

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IntaRNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand.

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miRNAkey

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are short abundant non-coding RNAs critical for many cellular processes. Deep sequencing (next-generation sequencing) technologies are being readily used to receive a more accurate depiction of miRNA expression profiles in living cells. This type of analysis is a key step towards improving our understanding of the complexity and mode of miRNA regulation.

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DSAP

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform.

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More complete gene silencing by fewer siRNAs

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Highly accurate knockdown functional analyses based on RNA interference (RNAi) require the possible most complete hydrolysis of the targeted mRNA while avoiding the degradation of untargeted genes (off-target effects). This in turn requires significant improvements to target selection for two reasons. First, the average silencing activity of randomly selected siRNAs is as low as 62%. Second, applying more than five different siRNAs may lead to saturation of the RNA-induced silencing complex (RISC) and to the degradation of untargeted genes.

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