A tool for mapping, naming, and quantifying tRNA-derived RNAs (tDRs). tDRmapper was designed specifically for human small RNA-seq data (single-end, 50x) generated on the Illumina sequencing platform using cDNA libraries that were prepared using the Illumina TruSeq protocol. It not only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel transfer RNAs and tRNA-derived RNA biology.
Facilitates the identification of tRNA-derived small RNA fragments (tRFs) to study their expression in cancers from deep-sequencing data with user-friendly interfaces and time-efficient algorithms. tRF2Cancer provides three useful tools for researchers to investigate tRFs. ‘tRFfinder’ is developed to identify genuine tRF signals from random degradation RNA fragments. One statistical method, the binomial test, is introduced to evaluate the significance of the abundance of sequenced sRNAs distributed on each tRNA. A classification method is subsequently used to annotate the types of tRFs based on their position of origin in pre-tRNA or mature tRNA; the four types of tRFs are tRF-5, tRF-3, tRF-1 and tRF-novel. ‘tRFinCancer’ enables users to inspect the expression of any tRFs in different types of cancers. ‘tRFBrowser’ presents both the sites of origin and the distribution of modification sites of tRFs, including m5C, 2′-O-Me, Ψ and m6A., on their corresponding source tRNA. In addition to cancer samples, tRFfinder can be applied to many samples from different kind of tissue/disease context.
A web application that allows you to detect and classify modified nucleotides in RNA-seq data. HAMR scans RNA-sequencing data for sites showing potential signatures of nucleotide modification. Simply point it to your RNA-seq data it will scan the entire transcriptome. You can also limit the analysis to particular genomic regions of interest, either by entering one or providing a BED file containing the intervals.
Identifies the subset of discovered transfer RNA fragments (tRFs) that could be originating outside of tRNA space and flags them as candidate false positives. MINTmap is a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNAseq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs.
Estimates potential RNA modification sites basing on nucleotide mismatches within sRNAs. SPORTS1.0 cleans reads by removing sequence adapters and discarding sequences with length beyond the defined range and those with bases other than ATUCG. It studies sequence mismatch information if mismatches are allowed during alignment process. This tool is useful in biomedical and evolution research that relate to sRNAs.
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