MiTie specifications


Unique identifier OMICS_01279
Name MiTie
Alternative name Mixed Integer Transcript IdEntification
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Jos Behr <>
  • person_outline Gunnar Rätsch <>
  • person_outline Jonas Behr <>

Publication for Mixed Integer Transcript IdEntification

MiTie in publications

PMCID: 4974672
DOI: 10.1002/jmrs.166

[…] results: the results demonstrated a 4.68% improved overall roleplay result when using vr to learn a specific task. the pre‐clinical survey results reveal 72% of these student (n = 59) found the vr mitie tool useful, however post survey results indicate only 32% (n = 62) were of the same opinion after experiencing the real clinical environment., conclusions: results indicate students […]

PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] of which cufflinks () is the most widely used. other methods are stringtie (), scripture (), trinity (), oases (velvet) (), soap-denovo-trans (), ireckon (), class (), flipflop (), isolasso (), mitie (), trans-abyss (), augustus (), traph ()., algorithms are classified by whether they use an alignment to a reference genome sequence, or whether they assemble the reads into full transcripts […]

PMCID: 4331715
PMID: 25708199
DOI: 10.1186/1471-2164-16-S2-S15

[…] rna-seq reads to the reference genome. after that, different algorithms can be used to infer transcripts from mapped reads, including cufflinks [,], isoinfer [], isolasso [], slide [], cliiq [], mitie [], etc. this ab initio approach is different from the de novo approach where reference genome is not used (such as abyss [], trinity [], etc.), and is able to take advantage of information […]



PMCID: 4282126
PMID: 27759933
DOI: 10.1002/jmrs.77

[…] sci 2014; 61: 159–165. doi: 10.1002/jmrs.60 , the authors would like to draw the reader's attention to an error in the following article:, the acknowledgements section should read as follows:, the mitie project was funded by health workforce australia as part of the simulated learning environments programme. the project was enhanced considerably by the collaborative support and input […]

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MiTie institution(s)
Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA; Friedrich Miescher Laboratory, Max Planck Society, Tubingen, Germany
MiTie funding source(s)
Supported by the German Research Foundation (grants RA1894/1-1 and RA1894/2-1), the Sloan-Kettering Institute and the Max Planck Society.

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