BaMM!motif statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BaMM!motif
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Tool usage distribution map

This map represents all the scientific publications referring to BaMM!motif per scientific context
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Associated diseases

This word cloud represents BaMM!motif usage per disease context
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Popular tool citations

chevron_left De novo motif discovery Motif enrichment analysis Motif comparison chevron_right
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Protocols

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


download.png
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

 (102)
library_books

Time resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

2018
BMC Biol
PMCID: 5937035
PMID: 29730990
DOI: 10.1186/s12915-018-0518-3

[…] network were supported by a network of TF binding, independently reconstructed from DNase-Seq data from Tregs (see ; Fig. ). Such comparison, however, is limited due to incompleteness of the binding motif database. The selected iTreg subnetwork (Fig. ) was enriched for genes of the TGF-β pathway, as indicated by functional enrichment analysis using Gene Ontology, KEGG, Reactome, and MSigDB Immuno […]

library_books

Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

2018
Nat Commun
PMCID: 5823854
PMID: 29472540
DOI: 10.1038/s41467-018-03082-6

[…] expressed in erythroid cells (175) were used for analysis of TF binding. For Fig. , differential motif enrichment was performed using HOMER’s findMotifs tool (v4.9, default parameters) using the same motif database as above.DiscSNPs that fell within TF binding peaks or DNase sites were tested for whether they disrupted a TF DNA motif as follows. A 40-bp window centered on the discSNP was scanned f […]

library_books

Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

2018
BMC Genet
PMCID: 5769447
PMID: 29334890
DOI: 10.1186/s12863-017-0596-1

[…] f 2, had 35 matches, 5 jolma2013, 5JASPERCORE2014 vertebrates and 25-uniprobe mouse. With MEME functional tool, we were able to affirm the similarities of our motifs to already published motif in the motif database. […]

library_books

Role of MAPK Signaling Pathways in Regulating the Hydrophobin Cryparin in the Chestnut Blight Fungus Cryphonectria parasitica

2017
PMCID: 5780368
PMID: 29371804
DOI: 10.5941/MYCO.2017.45.4.362

[…] moter region contained three types of binding motifs at a combined p-value of 8.41e-5 (). Motif 1 occurred five times and motifs 2 and 3 each occurred twice in the promoter region (). Using the yeast motif database SCPD, the motif database-scanning algorithm TOMTOM identified regulatory elements corresponding to binding motifs []. The regulatory elements corresponding to motif 1 were stress respon […]

call_split

Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10 clade

2017
BMC Plant Biol
PMCID: 5735953
PMID: 29258424
DOI: 10.1186/s12870-017-1210-4
call_split See protocol

[…] e between 6 and 18. TOMTOM [] was applied to the resulting MEME motifs using “Complete scoring” (which takes non-matching parts into account), and MEME motifs were compared with the JASPAR Core plant motif database [], and with the CIS-BP Arabidopsis thaliana database [].In addition to the de novo motif search, a set of potentially relevant existing motifs were obtained from literature [, ] and fr […]

library_books

Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway

2017
PLoS Comput Biol
PMCID: 5746249
PMID: 29240760
DOI: 10.1371/journal.pcbi.1005885

[…] e to these specific properties, the identification of linear motif sites is challenging both experimentally and computationally []. Currently, the most comprehensive collection, the Eukaryotic Linear Motif database (ELM) holds only 200–300 motif patterns with a few thousands of experimentally verified instances []. This number pales in comparison to the expected number of linear motif mediated int […]


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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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