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CrossLink

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

CrossLink is a versatile tool for the exploration of relationships between RNA sequences. After a parametrization phase, CrossLink delegates the determination of sequence relationships to established tools (BLAST, Vmatch and RNAhybrid) and then constructs a network. Each node in this network represents a sequence and each link represents a match or a set of matches. Match attributes are reflected by graphical attributes of the links and corresponding alignments are displayed on a mouse-click.

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Average: 5 (1 vote)

SAMMate

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

Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing this information.

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Average: 5 (1 vote)

sydSeq

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

In practice, identifying and interpreting the functional impacts of the regulatory relationships between micro-RNA and messenger-RNA is non-trivial. The sheer scale of possible micro-RNA and messenger-RNA interactions can make the interpretation of results difficult.

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Average: 5 (1 vote)

Automatic learning of pre-miRNAs from different species

Submitted by ChenLiang on Thu, 04/06/2017 - 17:26

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower.

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Average: 5 (1 vote)

si-shRNA Selector

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

Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in the results and the requirement for significant computational resources. Here we present a fast and practical algorithm for shRNA design based on the thermodynamic parameters.

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Average: 5 (1 vote)

mirdba

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

In silico generated search for microRNAs (miRNAs) has been driven by methods compiling structural features of the miRNA precursor hairpin, as well as to some degree combining this with the analysis of RNA-seq profiles for which the miRNA typically leave the drosha/dicer fingerprint of 1-2 ~22 nt blocks of reads corresponding to the mature and star miRNA. In complement to the previous methods, we present a study where we systematically exploit these patterns of read profiles.

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Average: 5 (1 vote)

SparseMFEFold

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

RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences.

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Average: 5 (1 vote)

OMICtools

Submitted by ChenLiang on Thu, 10/20/2016 - 20:44

Recent advances in 'omic' technologies have created unprecedented opportunities for biological research, but current software and database resources are extremely fragmented. OMICtools is a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics and metabolomics. All tools have been classified by omic technologies (next-generation sequencing, microarray, mass spectrometry and nuclear magnetic resonance) associated with published evaluations of tool performance.

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Average: 5 (1 vote)

pssRNAMiner

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

In plants, short RNAs including approximately 21-nt microRNA (miRNA) and 21-nt trans-acting siRNA (ta-siRNA) compose a 'miRNA --> ta-siRNA --> target gene' cascade pathway that regulates gene expression at the posttranscriptional level. In this cascade, biogenesis of ta-siRNA clusters requires 21-nt intervals (i.e. phasing) and miRNA (phase-initiator) cleavage sites on its TAS transcript. Here, we report a novel web server, pssRNAMiner, which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.

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Average: 5 (1 vote)

LimiTT

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

MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation of miRNA target interactions (MTIs) by high throughput screenings is challenging, as frequently used in silico target prediction tools are prone to emit false positives. This issue is aggravated for niche model organisms, where validated miRNAs and MTIs both have to be transferred from well described model organisms.

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5
Average: 4.5 (2 votes)

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