BaMM!motif statistics

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Citations per year

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Popular tool citations

chevron_left De novo motif discovery Motif enrichment analysis Motif comparison chevron_right
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BaMM!motif specifications

Information


Unique identifier OMICS_11505
Name BaMM!motif
Alternative names Bayesian Markov Model motif discovery, BaMMmotif2, BaMMmotif
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2
Stability Stable
Requirements
GCC, CMake, Boost, zoo, argparse, fdrtool, LSD, grid, gdata
Maintained Yes

Subtools


  • De-novo motif discovery
  • Motif database
  • Motif scan
  • Motif-motif comparison

Download


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github.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Johannes Soeding <>

Additional information


http://bammserver.readthedocs.io/en/latest/ The previous version can be found at https://github.com/soedinglab/BaMMmotif

Information


Unique identifier OMICS_11505
Name BaMM!motif
Alternative names Bayesian Markov Model motif discovery, BaMMmotif2, BaMMmotif
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Python
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Subtools


  • De-novo motif discovery
  • Motif database
  • Motif scan
  • Motif-motif comparison

Download


github.png

Documentation


Maintainer


  • person_outline Johannes Soeding <>

Additional information


http://bammserver.readthedocs.io/en/latest/ The previous version can be found at https://github.com/soedinglab/BaMMmotif

Publications for Bayesian Markov Model motif discovery

BaMM!motif citations

 (2)
library_books

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

2016
PMCID: 5291271
PMID: 27288444
DOI: 10.1093/nar/gkw521

[…] 83 s on a single core of a 3.4 ghz intel core i7-2600 cpu—we may choose a generous value k = 5 or even higher in practice., to further improve the performance of our bamm-based motif discovery tool bamm!motif, we will learn automatically from the data (i) the hyperparameters and (ii) the model length, a nontrivial task since the changing number of parameters precludes a simple optimization […]

library_books

Regulatory elements of Caenorhabditis elegans ribosomal protein genes

2012
PMCID: 3575287
PMID: 22928635
DOI: 10.1186/1471-2164-13-433

[…] by the current method., interestingly, these same four motifs were also found to be similar to characterized tf binding sites from c. elegans, human, drosophila, and yeast (figure ). we used three motif-motif comparison methods to find the similarities (stamp, matcompare, and tess), and found that they produced non-overlapping results. this finding indicates that in spite of the multitude […]


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BaMM!motif institution(s)
Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
BaMM!motif funding source(s)
Supported by the German Federal Ministry of Education and Research (BMBF) within the frameworks of e:Bio [SysCore, project 0316176A]; SPP 1935 (project CR 227/6-1) of the German Research Foundation (DFG); and the International Max Planck Research School for Genome Science (IMPRS-GS).

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