You are here

Home

C. elegans

Sfold

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

The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives of this software is to offer computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies.

Rating: 
5
Average: 5 (2 votes)

TargetBoost

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

We present a new microRNA target prediction algorithm called TargetBoost, and show that the algorithm is stable and identifies more true targets than do existing algorithms. TargetBoost uses machine learning on a set of validated microRNA targets in lower organisms to create weighted sequence motifs that capture the binding characteristics between microRNAs and their targets.

Rating: 
Average: 5 (1 vote)

NBmiRTar

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

Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this region of the mRNA target. Methods that do not rely on conservation generate numbers of predictions, which are too large to validate. We describe a target prediction method (NBmiRTar) that does not require sequence conservation, using instead, machine learning by a nave Bayes classifier.

Rating: 
Average: 5 (1 vote)

MiRAlign

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

MicroRNAs (miRNA) are approximately 22 nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in the secondary structure rather than in primary sequences.

Rating: 
Average: 5 (1 vote)

DIANA-mirExTra

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

High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer.

Rating: 
Average: 5 (1 vote)

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.

Rating: 
Average: 5 (1 vote)

ChIPBase

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

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity.

Rating: 
Average: 5 (1 vote)

E-RNAi

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

RNA interference (RNAi) has become a powerful genetic approach to systematically dissect gene function on a genome-wide scale. Owing to the penetrance and efficiency of RNAi in invertebrates, model organisms such as Drosophila melanogaster and Caenorhabditis elegans have contributed significantly to the identification of novel components of diverse biological pathways, ranging from early development to fat storage and aging.

Rating: 
Average: 5 (1 vote)

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.

Rating: 
Average: 5 (1 vote)

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.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to C. elegans