MINTmap – tRNA fragment (tRF) mapping tool

MINTmap¹ is a program, source code, and lookup table which can be used to generate tRF profiles from short RNA-Seq datasets. MINTmap is available under the open source GNU GPL v3.0 license. 

MINTmap download

Version: 1.0 (2/21/2017) – original version from publication

Version: 2.0-alpha (10/21/2021) – in response to many requests, we are making available a stable, pre-release version of MINTmap version 2.0-alpha.  This version can identify tRNA fragments (tRFs) that arise from the precursor tRNA sequence in addition to fragments from the mature tRNA.  For more details of the changes please visit our announcement.  

Explore all tRFs and tRF expression profiles in MINTbase

Our group has created MINTbase, a database for the interactive exploration of tRNA fragments and their expression profiles. We have made public various the tRF profiles of various projects, for example The Cancer Genome Atlas (TCGA) and the 1000 Genomes Project. MINTbase offers the user the opportunity to explore tRFs from various points of view. For every tRF, you can discover for example the expression per cancer, the reads per count (RPM), the parental tRNAs, and the datasets/tissues/diseases in which it is present. For every tRNA, you can view the fragments it produces per disease/tissue etc and the patterns of expression. Visit MINTbase to find out more about tRFs!

MINTmap TCGA profiles

You can find the MINTmap tRF profiles for TCGA in our TCGA tRF profiles page.

Other Resources

Our group has also created isoMiRmap, a mining tool for miRNAs and isomiRs.

References

1. Loher, P, Telonis, AG, Rigoutsos, I. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep. 2017;7 :41184. doi: 10.1038/srep41184. PubMed PMID:28220888 PubMed Central PMC5318995.
2. Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics. 2016;32 (16):2481-9. doi: 10.1093/bioinformatics/btw194. PubMed PMID:27153631 PubMed Central PMC4978933.