Tools and Downloads

Name Description Access
RNA22 RNA22 provides binding site predictions for miRNAs. Visit the following link to gain access to our pre-computed predictions, to visualize miRNA predictions, or to perform your own predictions interactively.
Mitochondrial and Nuclear tRNA fragments The MINT project offers a comprehensive tRNA fragment (tRF) analysis kit. Discover the tRFs in your dataset (or download tRF profiles of the datasets we analyzed), name your tRFs and discover their significance in the literature using the links.
Mitochondrial and Nuclear tRNA Lookalikes Loci of the genome that resemble known mitochondrial and nuclear tRNAs.
Off-Spotter Off-Spotter is a tool that when presented with a candidate gRNA and a PAM, quickly and exhaustively identifies all genomic sites that are identical or nearly-identical to the gRNA and also satisfy the PAM constraint. Read More.
Teiresias Teiresias ia a combinatorial algorithm for the discovery of rigid patterns (motifs) in biological sequences. Read More.
Threshold-seq R implementation of Threshold-seq, a computational method of determining thresholds for short RNA-seq datasets.
Novel miRNAs Coordinates, sequences, and RNA22 predictions for all identified novel miRNAs as described in this publication.
Pyknons A list of human and mouse pyknons with standardized nomenclature and a complete list of their genomics coordinates as described in this publication.
Platelets Access the data described in this 2014 publication and this 2012 publication.
CLIPSim-MC Access the data described in this publication.
Small RNA mouse datasets Next-gen datasets (gzipped tarball) mentioned in this publication.
HandsFree HandsFree is a secure service that provides the capability to map and analyze RNA-Seq, Exome-seq, DNA-seq, and ChIP-Seq data.
“Better Primer” A tool to help you design better primers.
Mirror of the UCSC Genome Browser Local installation of the very popular UCSC Genome Browser allows fast browsing, secure communication, etc.

*available only inside the TJU firewall

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