Targeted NGS for investigating the mitochondrial genome and heteroplasmy
Disrupted mitochondrial functions and genetic variants of mitochondrial DNA (mtDNA) have been observed in different human neoplasms. Next-generation sequencing (NGS) can be used to detect even low heteroplasmy-level mtDNA variants.…
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The miRBase Sequence Database – a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA registry.
The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results.
The miRBase Targets MicroCosm Targets (formerly miRBase Targets) is a web resource containing computationally predicted targets for microRNAs across many species. The miRNA sequences are obtained from the miRBase Sequence database and most genomic sequence from EnsEMBL.
The Plant MicroRNA Database – Our PMRD try to integrate the available large information of plant microRNAs data, consisting of microRNA sequence and their target genes, secondary dimension structure, expression profiling, genome browser, etc.
Patrocles – a database of polymorphic miRNA-target interactions. Patrocles compiles SNPs in the 3’UTR of human and mouse genes that either create or destroy miRNA target sites. miRNA target sites are defined as octamer motifs that are expected to show perfect Watson-Crick complementarity with the 5′ end of mature miRNAs.
GenomeTrafac – a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
miRDB – miRDB is an online database for miRNA target prediction and functional annotations in animals. All the targets were predicted by a bioinformatics tool called MirTarget2, which was developed by analyzing thousands of genes downregulated by miRNAs with an SVM learning machine. Common features associated with miRNA target binding have been identified and used to predict miRNA targets. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog and chicken.
microRNA Functional Analysis Tools
miRFocus: integrated pathway analysis of the miRNAome and the proteome.
MicroSNiPer : a web tool for prediction of SNP effects on putative microRNA targets. MicroSNiPer is a new web tool predicts the impact of a SNP on putative microRNA targets. This application interrogates the 3′-untranslated region and predicts if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. MicroSNiPer computes these sites and examines the effects of SNPs in real time. MicroSNiPer is a user-friendly web-based tool. Its advantages include ease of use, flexibility and straightforward graphical representation of the results.
TAM: A tool for annotations of microRNAs – The tool for annotations of human miRNAs (TAM) is a web-accessible program that is in the first version. TAM integrated miRNAs into different sets according to various rules and provides investigators with functions to mine potential biological meaning behind list of interested miRNAs.
MAGIA – (miRNA and genes integrated analysis) is a novel web tool for the integrative analysis of target predictions, miRNA and gene expression data. MAGIA is divided into two parts: the query section allows the user to retrieve and browse updated miRNA target predictions computed with a number of different algorithms (PITA, miRanda and Target Scan) and Boolean combinations thereof. The analysis section comprises a multistep procedure for (i) direct integration through different functional measures (parametric and non-parametric correlation indexes, a variational Bayesian model, mutual information and a meta-analysis approach based on P-value combination) of mRNA and miRNA expression data, (ii) construction of bipartite regulatory network of the best miRNA and mRNA putative interactions and (iii) retrieval of information available in several public databases of genes, miRNAs and diseases and via scientific literature text-mining.
SeqBuster – a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets. SeqBuster integrates multiple analyses modules in a unique platform and constitutes the first bioinformatic tool offering a deep characterization of miRNA variants (isomiRs). The application of SeqBuster to small-RNA datasets of human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some of them being associated to stem cell differentiation. The exhaustive description of the isomiRs provided by SeqBuster could help to identify miRNA-variants that are relevant in physiological and pathological processes.
MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server that integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters.
The miRò Ontology Database – a web-based knowledge base that provides users with miRNA–phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities.
EXPANDER (EXpression Analyzer and DisplayER) – is a java-based tool for analysis of gene expression data. Expander is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks. It includes microRNA target predictions for Human, Mouse, Fly, and C. elegans.
miRNAtools – This page is a compilation of several tools to analyze miRNA sequences, determine their targets and to analyze their possible roles in cellular metabolism. The user can follow TUTORIALS that show how to extract information on miRNA function by using real and theoretical examples.
SEQanswers – The next-generation sequencing community – threads tagged with miRNA.
microRNA Design Tools
WMD Version 3 – WMD3 is a web app for the automated design of artificial microRNAs. Artificial microRNAs (amiRNAs) are 21mer small RNAs, which can be genetically engineered and function to specifically silence single or multiple genes of interest in more than 90 plants, according to the previously determined parameters of target gene selection. It uses your favorite gene(s), which you want to silence, and designs 21mer amiRNA sequences. You will retrieve oligo sequences to express the small RNA from endogenous miRNA precursors.
microRNA Prediction Tools
miRecords is resource for animal miRNA-target interactions developed at the University of Minnesota. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs.
mirSVR scoring for predicted microRNA target sites – A new regression method for predicting likelihood of target mRNA down-regulation from sequence and structure features in microRNA/mRNA predicted target sites. MirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.
MiRror – A combinatorial analysis web tool for ensembles of microRNAs and their targets. The miRror application provides insights on microRNA (miRNA) regulation. It is based on the notion of a combinatorial regulation by an ensemble of miRNAs or genes. miRror integrates predictions from a dozen of miRNA resources that are based on complementary algorithms into a unified statistical framework. For miRNAs set as input, the online tool provides a ranked list of targets, based on set of resources selected by the user, according to their significance of being coordinately regulated. Symmetrically, a set of genes can be used as input to suggest a set of miRNAs. The user can restrict the analysis for the preferred tissue or cell-line. miRror is suitable for analyzing results from miRNAs profiling, proteomics and gene expression arrays.
Tapir – A web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA – target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA – target duplex having a large loop, making them undetectable by traditional tools.
PicTar is an algorithm for the identification of microRNA targets. This searchable website provides details (3′ UTR alignments with predicted sites, links to various public databases etc) regarding:
miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander (email@example.com).
TargetScan: Prediction of microRNA targets – Release 5.1 (April 2009). TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.
RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e.. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
miRNA – Target Gene Prediction at EMBL – This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. Both methods make use of genome comparison across insect species. Our 2005 predictions are based on pairing rules from a systematic experimental study (Brennecke & Stark et al., 2005) and have a very high sensitivity and specificity as assessed by experimental tests (see Supplement in Stark & Brennecke et al., 2005). We thus highly recommend to use the new predictions.
miRScan – Predict miRNA by analyzing a hairpin sequence
RegRNA – is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.
MicroInspector – A scanning software for detection of microRNA binding sites.
RNA22 – A pattern-based method for the identification of microRNA-target sites and their corresponding RNA/RNA complexes.
MiRAlign – MicroRNA Identification Based on Sequence and Structure Alignment.
miRU: Plant microRNA Potential Target Finder – The program predicts plant miRNA target genes. It reports all potential sequences complementary to the query with mismatches no more than specified for each mismatch type. In addition, each mismatch is penalized according to the mismatch type and position to the miRNA.
CrossLink – Visualization and exploration of sequence relationships between (micro) RNAs. After a parameterization phase, CrossLink uses the established tools BLAST, Vmatch and RNAhybrid to determine sequence relationships. Then, nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. Relationship attributes are reflected by labels and graphical attributes of each link and corresponding alignments pop up on a mouse-click. The type and number of links displayed can be adjusted interactively using value histograms and thresholds – taking a combination of dependencies on different relationship aspects into account. Powerful network layout operations and navigation capabilities complete the visualization features of this tool.
microRNA Analysis from Deep Sequencing Data
miRNAkey – A software pipeline for the analysis of microRNA Deep Sequencing data miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. This package implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple mapping levels, generating a novel platform for the analysis of miRNA expression.
Classification of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences.
Providing a detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag.
Discovery of the novel miRNAs from the high-throughput sequencing technology.
Identification of the differentially expressed miRNAs according to read tag counts (the number of reads for each tag reflects relative express level).
miRDeep – Discovering known and novel miRNAs from deep sequencing data. The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, …). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.
deepBase – a database for deeply annotating and mining deep sequencing data. A novel database, developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation.
miRExpress – Analyzing high-throughput sequencing data for profiling microRNA expression. A systematic method, for extracting miRNA expression profiles from sequencing reads generated by second-generation sequencing. miRExpress contains miRNA information from miRBase and efficiently reveals miRNA expression profiles by aligning sequencing reads against the sequences of known miRNAs. miRExpress can be used to find novel miRNA candidates by aligning reads with sequences of known miRNAs of various species.
miRanalyzer – A microRNA detection and analysis tool for next-generation sequencing experiments. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs.
CID-miRNA – Computational Identification of microRNA. A web server for identification of miRNA precursors in a given DNA sequence, utilizing secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form.