MDDLogo specifications

Information


Unique identifier OMICS_15001
Name MDDLogo
Interface Web user interface
Restrictions to use None
Input data A group of aligned DNA sequences.
Input format FASTA
Programming languages C++
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Tzong-Yi Lee <>

Publication for MDDLogo

MDDLogo in publications

 (4)
PMCID: 4895279
PMID: 26818115
DOI: 10.1186/s12918-015-0244-1

[…] differences in position-specific symbol compositions. the inherent complexity of large-scale ubiquitinome data may make it difficult to uncover conserved motifs. to overcome this problem, mddlogo [] was applied to identify potential motifs for the curated protein ubiquitination sites. mddlogo is a program that uses the maximal dependence decomposition (mdd) approach to discover […]

PMCID: 4290634
PMID: 25521204
DOI: 10.1186/1471-2105-15-S16-S1

[…] fragments of ser and thr residues for independent testing., in order to obtain substrate motif signatures of o-glcnacylation sites, the positive training data was analyzed by a motif analysis tool, mddlogo []. the mddlogo clustered a set of aligned o-glcnacylated sequences to divide a large group into subgroups that contain statistically significant substrate motifs. it has been suggested […]

PMCID: 4132336
PMID: 25147802
DOI: 10.1155/2014/528650

[…] motifs for large sets of sequences, we applied maximal dependence decomposition (mdd) [] to cluster all sequences of acetylation site into subgroups containing statistically conserved motifs. mddlogo, a tool implementing mdd, has reported that the grouping of protein sequences into smaller groups should be done prior to computationally identifying ptm sites [–]. mddlogo adopts […]

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

[…] dependencies between positions. previous studies , have proposed the grouping of protein sequences into smaller groups prior to creating prediction models. for this study, mdd is applied using mddlogo . mdd adopts chi-square test to evaluate the dependence of amino acid occurrence between two positions, ai and aj, which surround the phosphorylation site. in order to extract motifs […]


To access a full list of publications, you will need to upgrade to our premium service.

MDDLogo institution(s)
Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, Taiwan
MDDLogo funding source(s)
This work was supported by the National Science Council of the Republic of China under Contract Numbers of NSC 99-2320-B-155-001.

MDDLogo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MDDLogo