You are here

Home

Fruitfly

piRNA cluster database

Submitted by ChenLiang on Sun, 01/08/2017 - 16:30

Piwi proteins and their guiding small RNAs, termed Piwi-interacting (pi-) RNAs, are essential for silencing of transposons in the germline of animals. A substantial fraction of piRNAs originates from genomic loci termed piRNA clusters and sequences encoded in these piRNA clusters determine putative targets for the Piwi/piRNA system. In the past decade, studies of piRNA transcriptomes in different species revealed additional roles for piRNAs beyond transposon silencing, reflecting the astonishing plasticity of the Piwi/piRNA system along different phylogenetic branches.

Rating: 
Average: 5 (1 vote)

siRNAmod

Submitted by ChenLiang on Sun, 01/08/2017 - 16:41

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking.

Rating: 
Average: 5 (1 vote)

ZooMir

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

MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides. Thousands of miRNA genes have been identified (computationally and/or experimentally) in a variety of organisms, which suggests that miRNA genes have been widely shared and distributed among species. Here, we used unique miRNA sequence patterns to scan the genome sequences of 56 bilaterian animal species for locating candidate miRNAs first.

Rating: 
Average: 5 (1 vote)

ncPRO-seq

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

Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs.

Rating: 
Average: 5 (1 vote)

mirExplorer

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

microRNAs (miRNAs) represent an abundant group of small regulatory non-coding RNAs in eukaryotes. The emergence of Next-generation sequencing (NGS) technologies has allowed the systematic detection of small RNAs (sRNAs) and de novo sequencing of genomes quickly and with low cost. As a result, there is an increased need to develop fast miRNA prediction tools to annotate miRNAs from various organisms with a high level of accuracy, using the genome sequence or the NGS data. Several miRNA predictors have been proposed to achieve this purpose.

Rating: 
Average: 5 (1 vote)

miRNA-SNiPer

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

MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Previous studies have proven that genetic variability of miRNA genes (miR-SNP) has an impact on phenotypic variation and disease susceptibility in human, mice and some livestock species. MicroRNA gene polymorphisms could therefore represent biomarkers for phenotypic traits also in other animal species.

Rating: 
Average: 5 (1 vote)

mircisreg

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

MicroRNAs are a class of endogenous small RNAs that play regulatory roles. Intergenic miRNAs are believed to be transcribed independently, but the transcriptional control of these crucial regulators is still poorly understood.

Rating: 
Average: 5 (1 vote)

NRDR

Submitted by ChenLiang on Thu, 10/20/2016 - 20:36

Large-scale transcriptome projects have shown that the number of RNA transcripts not coding for proteins (non-coding RNAs) is much larger than previously recognized. High-throughput technologies, coupled with bioinformatics approaches, have produced increasing amounts of data, highlighting the role of non-coding RNAs (ncRNAs) in biological processes. Data generated by these studies include diverse non-coding RNA classes from organisms of different kingdoms, which were obtained using different experimental and computational assays.

Rating: 
Average: 5 (1 vote)

miRdentify

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

During recent years, miRNAs have been shown to play important roles in the regulation of gene expression. Accordingly, much effort has been put into the discovery of novel uncharacterized miRNAs in various organisms. miRNAs are structurally defined by a hairpin-loop structure recognized by the two-step processing apparatus, Drosha and Dicer, necessary for the production of mature ~ 22-nucleotide miRNA guide strands.

Rating: 
Average: 5 (1 vote)

Geoseq

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

Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Fruitfly