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MAMOT specifications


Unique identifier OMICS_28922
Alternative name hidden MArkov MOdelling Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Mauro Delorenzi
  • person_outline Frederic Schutz

Publication for hidden MArkov MOdelling Tool

MAMOT citations


Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan

PLoS One
PMCID: 5365146
PMID: 28339501
DOI: 10.1371/journal.pone.0174749

[…] ching barcode records from the Pakistan specimens with those already on BOLD. Specimen information, collection data, and specimen images were submitted to BOLD and are available under the dataset, DS-MAMOT which can be accessed through the following DOI ( […]


Nuclear Factor I genomic binding associates with chromatin boundaries

BMC Genomics
PMCID: 3610271
PMID: 23402308
DOI: 10.1186/1471-2164-14-99

[…] atrix (shown as a sequence logo in Figure E). This logo was derived from 5,579 25bp-long NFI binding sequences obtained with a SELEX-SAGE experiment [], using the hidden Markov model-training program MAMOT (Schütz and Delorenzi 2008) to iteratively optimize a weight matrix model starting from the consensus sequence TTGGCNNNNNGCCAA. Applying the same procedure to 4,794 200bp-long sequences centered […]


HMMConverter 1.0: a toolbox for hidden Markov models

Nucleic Acids Res
PMCID: 2790874
PMID: 19740770
DOI: 10.1093/nar/gkp662

[…] ynamic programming. HMMER3 () is a software package for automatically deriving profile HMMs from given multiple-sequence alignments such as those of the protein family data base Pfam (). HMMoc () and MAMOT () are the two most recent developments and the first to explicitly cater for probabilistic models. MAMOT is a compiler that can be used to set up simple HMMs, but not generalized HMMs and pair- […]


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MAMOT institution(s)
Swiss Institute of Bioinformatics and Bioinformatics Core Facility of the NCCR Molecular Oncology, Lausanne, Switzerland
MAMOT funding source(s)
Supported by National Centre for Competence in Research (Molecular Oncology), Swiss National Science Foundation.

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