Summary SamQL implements a SQL-like query language for filtering and extracting reads from SAM/BAM alignment files based on arbitrary combinations of alignment attributes. The tool enables complex queries that are not possible with existing SAM/BAM filtering utilities, facilitating flexible downstream analysis of sequencing data.
Summary bíogo is a bioinformatics library written in the Go programming language, providing high-performance tools for common genomic data processing tasks. The toolkit offers a clean API for sequence manipulation, alignment, and genomic data parsing with the performance characteristics of a compiled language.
Summary CLIPSeqTools is a modular bioinformatics pipeline for the analysis of CLIP-seq data, providing tools for read processing, peak calling, motif analysis, and visualization. The suite enables comprehensive characterization of RNA-binding protein interaction sites across the transcriptome.
Summary DIANA-LncBase is the first database dedicated to microRNA interactions with long non-coding RNAs, combining experimentally validated interactions with high-confidence computational predictions. The resource enables systematic study of miRNA-lncRNA regulatory networks.
Summary DIANA miRPath v.2.0 enables researchers to study how multiple microRNAs cooperatively regulate biological pathways. The updated tool incorporates improved statistical methods and expanded databases for pathway enrichment analysis based on miRNA target predictions.
Summary This study demonstrates that microRNAs can regulate gene expression through binding sites located within protein-coding sequences, not only the canonical 3’ UTR sites. Functional coding sequence targets are identified and validated, broadening the scope of miRNA-mediated gene regulation.
Summary TarBase 6.0 is a manually curated database of experimentally validated microRNA targets, significantly expanding the collection of miRNA-target interactions with experimental support from the literature. The database provides a gold standard for benchmarking computational prediction methods.
Summary This update to the DIANA-microT web server extends its target prediction capabilities to Drosophila melanogaster and Caenorhabditis elegans microRNAs, and introduces a bibliographic module linking microRNAs to diseases based on the scientific literature.
Summary This article provides a curated overview of the online tools, databases, and web servers available for microRNA research, covering target prediction, expression analysis, and pathway analysis resources.
Summary DIANA-mirExTra identifies microRNAs driving observed gene expression changes by combining miRNA target predictions with gene expression data. Users provide a list of differentially expressed genes and receive ranked microRNAs predicted to regulate that expression signature.
Summary This work provides a systematic assessment of the state of computational microRNA target identification, examining the performance of existing tools and discussing the challenges in translating predictions into biological insight. Guidelines are provided for researchers interpreting computational miRNA target predictions.
Summary This study benchmarks microRNA target prediction methods against protein repression data, showing that the DIANA-microT algorithm achieves high correlation with experimentally measured protein repression. The work provides a framework for evaluating and improving computational miRNA target prediction.
Summary DIANA-mirPath is a web-based tool that integrates microRNA target predictions with KEGG pathway data to identify biological pathways regulated by user-specified microRNAs. The tool supports both human and mouse miRNAs and provides statistical analysis of pathway enrichment.
Summary The DIANA-microT web server provides access to the DIANA-microT algorithm for microRNA target prediction. The server enables researchers to identify genes regulated by specific microRNAs, query microRNAs targeting specific genes, and perform pathway-level analysis of miRNA regulatory networks.