Tools and Algorithms

RiboTempo [download here (EXE)] (requires .NET Framework 4.5.2 or higher)
Program to calculate ribosome occupancy
Zhang G, Hubalewska M, Ignatova Z. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol. 2009 Mar;16(3):274-80.
https://pubmed.ncbi.nlm.nih.gov/19198590/

human tRNA-concentrations [download here (ZIP)]
Table for total concentrations
Polte C, Wedemeyer D, Oliver KE, Wagner J, Bijvelds MJC, Mahoney J, de Jonge HR, Sorscher EJ, Ignatova Z. Assessing cell-specific effects of genetic variations using tRNA microarrays. BMC Genomics. 2019 Jul 16;20(Suppl 8):549.
https://pubmed.ncbi.nlm.nih.gov/31307398/

Github:
ADAM-tRNA-Seq
RNA-based barcode de-multiplexing pipeline for direct sequencing of tRNA using Nanopore
Alarcon R, Köster D, Behrmann S, Ignatova Z. ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing. Nucleic Acids Res. 2026 Jan 22;54(3):gkag022.
https://pubmed.ncbi.nlm.nih.gov/41574434/