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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




No version available


  • person_outline Jos Behr
  • person_outline Gunnar R├Ątsch
  • person_outline Jonas Behr

Publication for Mixed Integer Transcript IdEntification

MiTie citations


Benchmark analysis of algorithms for determining and quantifying full length mRNA splice forms from RNA seq data

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

[…] data, 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 de n […]


Accurate inference of isoforms from multiple sample RNA Seq data

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

[…] ibly due to intron retention, non-coding RNAs or other unknown mechanisms [].We compared the performance of ISP with two existing assembly algorithms for multiple samples, Cufflinks/Cuffmerge [,] and MITIE []. Cufflinks and Cuffmerge are algorithms incorporated in the Cufflinks software package. For multiple RNA-Seq samples, Cufflinks first constructs a set of isoforms from multiple samples, follo […]


The development and evaluation of a medical imaging training immersive environment

PMCID: 4175849
PMID: 26229652
DOI: 10.1002/jmrs.60

[…] The MITIE simulation environment was created by End-to-End Visuals using the Quest3D runtime library. Quest3D is an advanced real-time development platform that leverages the Microsoft DirectX API. Quest3 […]


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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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