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MMSEQ | Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

Provides a statistical method allowing haplotype, isoform and gene specific expression evaluation. MMSEQ is a package that takes into account of various features such as multi-mapping of reads, including mapping to transcripts from different genes and sequence-specific biases. It can be used for analyzing differential expression or quantify the abundance of known transcripts. The application also can be downloaded as part of the ArrayExpressHTS software.

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MMSEQ classification

MMSEQ specifications

Unique identifier:
Command line interface
Input format:
Programming languages:
C, C++, R, Ruby, Shell (Bash)
Computer skills:
Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS
GNU General Public License version 2.0
Boost C++ libraries, GNU Scientific Library, Armadillo C++ linear algebra library, SAMtools library

MMSEQ distribution


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MMSEQ support



  • Ernest Turro <>


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Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Department of Haematology, University of Cambridge, NHS Blood and Transplant, Cambridge, UK; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal QC, Canada

Funding source(s)

Supported by Cancer Research UK grant C14303/A10825, the Cambridge Biomedical Research Centre, by UK BBSRC grant BB/E020372/1 and a Team Grant from the Fonds de recherche du Quebec—Nature et technologies.

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