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T-Aligner specifications


Unique identifier OMICS_25643
Name T-Aligner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A graphical representation of the alignments: a dot matrix showing editing states (number of Ts) at each site.
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Version 3.0
Stability Stable
Qt library
Maintained Yes




No version available


  • person_outline Sara Zimmer <>
  • person_outline Pavel Flegontov <>

Publication for T-Aligner

T-Aligner citation


Gene Loss and Error Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid

PMCID: 4669381
PMID: 26628723
DOI: 10.1128/mBio.01498-15

[…] the final edited product, as reads edited over the entire length lacked seeds long enough for initial mapping., to overcome the problem of missing seeds, we developed a novel read mapping tool, t-aligner, based on the smith-waterman algorithm and designed to mimic the 3′-to-5′ progression of rna editing in kinetoplastids. initially, a fixed seed is chosen in a never-edited or universally […]

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T-Aligner institution(s)
Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia; Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Science, University of South Bohemia, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia; Russia Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia; Skolkovo Institute of Science and Technology, Moscow, Russia; Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
T-Aligner funding source(s)
Supported by European Research Council CZ [LL1601]; Czech Science Foundation [15-21974S, 17-10656S, 16-18699S]; University of Ostrava IRP project “New research directions in the Life Science Research Centre”; Moravian–Silesian Region [research programs 2013–2014 and 2015, DT01-021358]; Czech Ministry of Education, Youth and Sports [LO1208 “TEWEP”]; Russian Science Foundation [transcriptomic library sequencing was supported by 14-50-00029]; Russian Foundation for Basic Research [14-04-01717]; American Heart Association [16SDG26420019]; University of Minnesota Genomics Center Pilot Project Award and an Alexander Dubcek Fund travel fellowship (University of Minnesota).

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