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MoDL specifications

Information


Unique identifier OMICS_24120
Name MoDL
Alternative name Motif Description Length
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some phosphopeptides.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Benjamin Raphael
  • person_outline Anna Ritz

Publication for Motif Description Length

MoDL citations

 (3)
library_books

Identifying Protein Phosphorylation Sites with Kinase Substrate Specificity on Human Viruses

2012
PLoS One
PMCID: 3402495
PMID: 22844408
DOI: 10.1371/journal.pone.0040694

[…] he chickenpox virus, on S224 of the IE63 protein.To demonstrate the effectiveness of MDD clustering method, the MDD-detected motifs are compared with two well-known motif discover tools, Motif-X and MoDL . and show that MDD could identify new motifs for viral protein phosphorylation sites and is comparable to other methods. As shown in , MDD is able to detect five motifs from the available viru […]

call_split

Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis

2011
PLoS One
PMCID: 3102080
PMID: 21647451
DOI: 10.1371/journal.pone.0020025
call_split See protocol

[…] In this study we have performed four sets of experiments to compare the motif-discovery ability of F-Motif with that of Motif-X and MoDL. In one of our experiments, as our foreground data we have collected only the serine-phosphorylated peptides of length 13 (i.e., 13-mers centered at serine) from the Phospho.ELM database (Version […]

library_books

Motif All: discovering all phosphorylation motifs

2011
BMC Bioinformatics
PMCID: 3044277
PMID: 21342552
DOI: 10.1186/1471-2105-12-S1-S22

[…] e peptides matching the motif identified in the first round are removed prior to the second round of searching. This procedure repeats a number of rounds until no significant motifs can be found. The MoDL method [] is an optimization-based algorithm, which formulates the motif-finding problem as the minimization of description length. In other words, MoDL tries to optimize the expressiveness of a […]

Citations

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MoDL institution(s)
Department of Computer Science, Brown University, Chicago, IL, USA; Toyota Technological Institute at Chicago, Chicago, IL, USA; Department of Chemistry and Molecular Biology, Cell Biology, and Biochemistry, Providence, RI, USA; Center for Computational Molecular Biology, Brown University, Providence, RI, USA
MoDL funding source(s)
Supported by Career Award at the Scientific Interface from the Burroughs Wellcome Fund; National Institutes of Health (grant 2P20RR015578); Beckman Young Investigator Award; NSF Graduate Fellowship.

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