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MDscan specifications

Information


Unique identifier OMICS_06288
Name MDscan
Alternative name Motif Discovery scan
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_06288
Name MDscan
Alternative name Motif Discovery scan
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Motif Discovery scan

MDscan citations

 (50)
library_books

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation

2017
eLife
PMCID: 5451215
PMID: 28562241
DOI: 10.7554/eLife.23645.026

[…] DNA sequence of ±100 bp around the summit of the top 200 SDC-2 ChIP-seq binding peaks was used to identify potential binding motifs using MDScan (). The position weight matrix of the top motif was used to scan and score the whole genome using TRAP (). Resulting TRAP affinity scores were standardized to a 0 to 10 scale. Motif locations a […]

library_books

An integrative and applicable phylogenetic footprinting framework for cis regulatory motifs identification in prokaryotic genomes

2016
BMC Genomics
PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] (CUBIC) are 25.3 % in nPC, 8.1 % in nCC, 35.7 % in sFS and 38.6 % in sASP. It is worth noting that, even though MicroFootprinter provides much fewer results, its predictions have higher specificity. MDscan had a relatively higher performance than the other published tools. MDscan starts on an enumeration strategy on the top several sequences, which is more adaptable to the data of phylogenetic fo […]

library_books

Nuc‐ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination

2016
Glia
PMCID: 5021170
PMID: 27017927
DOI: 10.1002/glia.22977

[…] ing the command‐line version of WebMotifs (Romer et al., ). The set of 75 peak sequences was used in three different motif discovery programs: AlignACE (Hughes et al., ), Weeder (Pavesi et al., ) and MDscan (Liu et al., ). Over‐represented motifs were identified by these programs in the peak sequences relative to a background distribution, which later was compiled from the entire 15,912 promoter s […]

library_books

Transcription factor motif quality assessment requires systematic comparative analysis

2016
F1000Res
PMCID: 4821295
PMID: 27092243
DOI: 10.5256/f1000research.7983.r11604

[…] ocessing as well as the assessment techniques used in each motif discovery pipeline. POUR motifs are learned from full-length sequences of the top 250 peaks using five motif finding algorithms (MEME, MDscan, Trawler, AlignAce and Weeder) , the ZLAB group used 100bp of the top 500 sequences centred on the ChIP-seq peaks using MEME-ChIP , while GUERTIN reports the top 5 motifs for each technique gen […]

library_books

Genome Wide De Novo Prediction of Cis Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv

2016
PLoS One
PMCID: 4757040
PMID: 26886880
DOI: 10.1371/journal.pone.0148965

[…] t. Secondly, Midha et al. used only one motif finding tool (MEME) to uncover motifs, whereas we included, in addition to MEME, four other complementary motif-finding algorithms (BioProspector, CUBIC, MDscan and MotifSampler) in our analyses. These five algorithms exhibit complementary prediction effect and collectively lead to more accurate prediction of true binding sites []. Finally, Midha et al […]

library_books

ERG signaling in prostate cancer is driven through PRMT5 dependent methylation of the Androgen Receptor

2016
eLife
PMCID: 4909395
PMID: 27183006
DOI: 10.7554/eLife.13964.024

[…] genome version Hg19 using BWA, and binding sites (‘peaks’) were identified using MACS2, evolutionary conservation scores at peak locations was calculated using Phastcons and enriched DNA motifs using MDscan and Seqpos. These were performed using the ChiLin QC pipeline (liulab.dfci.harvard.edu/WEBSITE/software). Peaks from AR ChIP-sequencing samples with a MACS2 enrichment score higher than 10 were […]

Citations

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MDscan institution(s)
Stanford Medical Informatics, Stanford University, Stanford, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA; Department of Statistics, Harvard University, Cambridge, MA, USA

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