DiMO specifications

Information


Unique identifier OMICS_02190
Name DiMO
Alternative name Discriminative Motif Optimizer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.6
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Ronak Patel
  • person_outline Gary Stormo

Publication for Discriminative Motif Optimizer

DiMO citations

 (2)
library_books

Comparison of discriminative motif optimization using matrix and DNA shape based models

2018
BMC Bioinformatics
PMCID: 5840810
PMID: 29510689
DOI: 10.1186/s12859-018-2104-7

[…] by DAMO, a perceptron-based optimization method that finds the optimal PWM with the highest area under the receiver operating characteristic curve (AUROC). DAMO is similar to our previously described DiMO [], but where DiMO provided optimized PFMs, DAMO provides optimized PWMs which have recently been shown to avoid the inherent limitations of probabilistic models []. DAMO also allows for the incl […]

library_books

Direct AUC optimization of regulatory motifs

2017
Bioinformatics
PMCID: 5870558
PMID: 28881989
DOI: 10.1093/bioinformatics/btx255

[…] rmance of CDAUC is systematically evaluated. As one of the most widely used DML methods, DREME was firstly adopted to identify the preliminary motifs, these motifs were then re-optimized by CDAUC and DIMO separately. The outputs of three methods were then compared to assess CDAUC for optimizing DML motifs. In addition, we also adopted HOMER as a comparison baseline.We downloaded the ChIP-seq data […]

DiMO institution(s)
Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
DiMO funding source(s)
Supported by NIH (HG000249).

DiMO reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DiMO