Discovers genes involved in a biological process. RNAiCut employs the connectivity of subgraphs of protein-protein interaction (PPI) networks to find score thresholds from functional genomic data. It allows hit-list gene selection with orthogonal datasets. This tool calculates the edge count of induced subgraph and determines the P-value of finding a PPI subgraph. It is useful for functional genomics research.
Identifies, predicts and characterizes noncoding RNAs (ncRNAs). incRNA is a machine learning framework which integrates sequence, structure, and expression data. The software was used, with data from the modENCODE consortium, to separate known C. elegans ncRNAs from coding sequences and other genomic elements and find more than 7000 novel ncRNA candidates, among which more than 1000 were located in the intergenic regions of C. elegans genome.
Finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, etc.) by computing all semi-global alignments. GotohScan is a computationally sensitive full dynamic programming approach. Thus, the query sequence is never truncated or split into sub-sequences, but always mapped to the database over its complete length. The alignment is computed via the Gotoh-alignment algorithm using affine gap costs.
A clustering method that efficiently identifies noncoding RNA (ncRNA) elements in a bacterial genome. This web server enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments.
Performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data. RandA reveals the complexity of the ncRNA repertoire in a given cell population. It maps the reads against the newly formed database using a Burrows–Wheeler transform based alignment tool summing the number of reads that mapped uniquely to each of the annotated ncRNA sequence. The tool produces a table comprising of all the mapped ncRNAs in a given sample.
Predicts the pathogenicity of single nucleotide substitutions in human mitochondrial tRNA (mt-tRNA) variations. PON-mt-tRNA arranges the variations with the maximum likehood (ML) method and has a 2-fold importance for diagnosing the pathogenicity of mt-tRNA variations. It classifies variations into five classes: neutral, likely neutral, pathogenic, likely pathogenic and variants of uncertain significance.
Predicts siRNA off-target interactions and enables off-targeting potential comparisons between different siRNA designs. siRNA off-target discovery pipeline can predict the off-target transcripts and compute the off-targeting potential of a given siRNA in human. This pipeline can easily be tuned for any other organism by simply replacing the input data. This tool is able to calculate siRNA off-targeting potentials on an entire human genome/transcriptome in the time scale of hours thanks to the large-scale prediction capabilities of RIsearch.
Identifies active microRNA transcription start sites (miRNA TSSs) from nascent transcriptomes. MirSTP provides accurate TSS prediction for human intergenic miRNAs at a high resolution by using characteristic bidirectional transcription signatures. It can be applied to any cell line or condition with available Global nuclear run-on (GRO)/precision nuclear run-on sequencing (PRO-seq) data.
Analyzes miRNA next generation sequencing (NGS) data. MiRMaster performs the most frequently requested applications and aims to help in searching for novel miRNA candidates, quantifying miRNA expression and identifying isoforms and variants of miRNAs. Besides, the application can proceed the mapping of non-human small RNA reads against the NCBI RefSeq collection of bacterial and viral genomes to detect contaminations, infections or exogenous miRNAs.
Infers gene-specific contributions to phenotypes in RNA interference screens. PheLiM proceeds by integrating predictions of on- and off- target small interfering RNA-(siRNA) induced down-regulation. It can discover validated targets and related potentially new regulators from different screens that calculated several phenotypes. This tool achieves better results when the prediction accuracy on seed-disjoint validation datasets are maximized.
Allows users to determine long non-coding RNA (lncRNA) interactions using four models for lncRNA regulation. LongHorn is a pan-cancer analysis of lncRNA regulatory interactions. This tool is able to detect four models for lncRNA regulation: decoy (binds and inhibits the activity of effectors); co-factor (binds proximal promoters of protein-coding genes and alter their regulation by transcription factors (TFs)); guide (simplifies regulation of protein-coding genes by TFs); and switch (alters the activity of TFs and RNA-binding proteins (RBPs) across multiple targets).
Supports the translation of micro-RNAs (miRNAs). miRNACon is a web application that permits users to test individual miRNAs or miRNA signatures for likelihood of being influenced. This tool proceeds in five steps where researchers have to: (1) select miRBase version; (2) select miRNA identifier; (3) enter parameters related to age; (4) select probe type; and (5) place their input for realizing the computation.
Performs an automatic recognition of blocks of reads. blockbuster is based on an algorithm that replaces each read by Gaussian profile centered at the midpoint of the read. The application can be employed to verify miRs and miRs* position between annotation and short-read data as well as for identifying their associated expression levels. The software accepts files from the segemehl software and can be used in conjunction with it.
Allows users to score high two Infernal covariance models. CMCompare is an extendable polynomial-time algorithm that furnishes information for: (i) determining the high discriminative power of a model against other ones; (ii) localizing which regions of the model overlap with another; (iii) obtaining a natural similarity score for RNA families. It aims to help in selecting models as well as check relationships between them.
Detects genes and other potentially functional sequences that may be missed by standard ORF-calling, RNA finding, and pattern matching software. Tricross produces a multi-way cross comparison of three sets of sequences, determine which are conserved in all three sets, and produce a graphical representation as well as alignments of all sequence triples found.
Identifies the binding sites of RNA molecules. RBind transforms the RNA tertiary into a network, where nucleotides are nodes, and their non-covalent interactions with each other are the edges. It recognizes binding sites by determining the degree values for short-range binding cavity and closeness values for long-range allosteric effect. This tool is useful to find critical nucleotides for binding.
Enables researchers to predict the origin site of tumor samples of their interests. MMCOP is a web-server that consists of classifiers based on Illumina 450k DNA methylation (DNAm) profiles and microRNA (miRNA) expression. 14 tissues for miRNA expression profiles are supported by the software, as well as the same number for DNA methylation profiles. The software was tested using seven DNAm datasets in GEO.
Resolves ambiguous mappings on the basis of a statistical model that can be customized by the user. bcSeq is an open source R package for mapping reads from high-throughput shRNA and sgRNA sequencing assays based on a default or a user-defined Phred score-based probability model. It accommodates sequences of varying lengths and provides the option of using Hamming or edit distance. It can also tolerate mismatches, internal insertions and deletions.
Permits users to detect ping-pong cycle activity in small RNA-Seq data. PingPongPro is an application that locates sites of piRNA-mediated cleavage and identifies transposons suppressed through the ping-pong cycle. This method takes additional covariates into account and auto-tunes its parameters to the data. It is built on the next-generation sequencing (NGS) analysis library SeqAn.