Functional RNAs

This section contains information on various functional RNAs. Included are tRNAs, non-coding RNAs, rRNAs and snoRNAs.

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ComiRTool Content

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ComiR is a web tool for combinatorial microRNA (miRNA) target prediction. Given an messenger RNA (mRNA) in human, mouse, fly or worm genomes, ComiR predicts whether a given mRNA is targeted by a set of miRNAs.

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CopraRNA and IntaRNATool Content

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CopraRNA and IntaRNA webserver tools: CopraRNA is a tool for sRNA target prediction, while IntaRNA enables the prediction of RNA-RNA interactions.

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corRnaTool Content

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corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.

CrossLinkTool Content

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Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

DARIOTool Content

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DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.

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DIANA miRPathTool Content

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DIANA miRPath v2.0 is a web-based computational tool that identifies potentially altered molecular pathways by the expression of a single or multiple microRNAs.

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DIANA-microT v5.0Tool Content

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The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser. Updates include sophisticated workflows.

DSAPTool Content

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Deep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.

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DSAP: deep-sequencing small RNA analysis pipeline201015

Freiburg RNA ToolsTool Content

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The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

IntaRNATool Content

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IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.

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MAGIA2Tool Content

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miRNA and Genes Integrated Analysis (MAGIA2) is a web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene expression data.

MAGNOLIATool Content

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MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern.

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