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Matcompare specifications


Unique identifier OMICS_22472
Name Matcompare
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Dustin Schones <>
  • person_outline Kevin Harrod <>

Publications for Matcompare

Matcompare citations


Synergistic co regulation and competition by a SOX9 GLI FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions

PMCID: 5919691
PMID: 29659575
DOI: 10.1371/journal.pgen.1007346

[…] regulators, we performed de novo motif enrichment analysis in the promoter regions for the genes in each cluster using the computer program discriminating motif enumerator (dme), motifclass and matcompare [–]. the most enriched tf binding motifs include sox9 and gli (gli1, gli2 and gli3) in the pz and phz; sox9/foxa and klf4 in the uhz; and mef2c and foxa motifs in the lhz (). the core […]


Regulatory elements of Caenorhabditis elegans ribosomal protein genes

PMCID: 3575287
PMID: 22928635
DOI: 10.1186/1471-2164-13-433

[…] 12–0 is not likely to be a gaga-factor binding site []., all nine motifs were compared to known sites from a wide variety of tf binding sequence databases using three comparison methods: stamp [], matcompare [], and tess []. motif 12–5 was found by matcompare to be similar to transfac tcf1-like matrix m00362, a binding site of the drosophila hmg box-containing factor pan [,]. c. elegans […]


Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain

PMCID: 3315485
PMID: 22496663
DOI: 10.1371/journal.pgen.1002614

[…] we we generated energy-based position weight matrices and logos (), and calculated the degree of similarity between all matrices as kullback-leibler divergences (kld) using the program matcompare (see ). a kld generally indicates that two matrices are significantly similar, and a kld of 0 indicates that they are identical. all measured binding affinities, position weight matrices, […]


A Systems Biology Approach to Transcription Factor Binding Site Prediction

PMCID: 2845628
PMID: 20360861
DOI: 10.1371/journal.pone.0009878

[…] the most co-expressed targets are considered., for each tf, the single most enriched motif was compared to the transfac reported motifs for that tf. success was reported if a match was found using matcompare . the recall rate for conservation-free, co-expression, and co-expression*, was 27/70 (39%), 13/70 (19%), and 25/70 (36%), respectively (). in our experiments, aracne (conservation-free […]


Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

PMCID: 2790884
PMID: 19767611
DOI: 10.1093/nar/gkp747

[…] independently using each background training set, and motifs identified in all three runs were selected. corresponding motifs between runs were identified by high matrix similarity determined using matcompare () (most had identical consensus sequences and similar enrichment scores among the three runs computed by dme2). as expected, almost all the motifs discovered by this process show a level […]


An integrative genomics approach identifies Hypoxia Inducible Factor 1 (HIF 1) target genes that form the core response to hypoxia

PMCID: 2724271
PMID: 19491311
DOI: 10.1093/nar/gkp425

[…] was employed using the zoops model to identify motifs of length 5–12 bases compared to a background set. only the top 50 enriched motifs were reported and compared to known motifs using the program matcompare in cread ()., the program storm in cread (,) was used to match pwms to genomic dna and was employed using a p-value cutoff of 1e-4. this cutoff was found to be optimal since a cutoff of p […]

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Matcompare institution(s)
Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
Matcompare funding source(s)
Supported by NIH HL071547 and HL06779 (K.S.H), NIH Minority Post-doctoral supplement and NIH HG001696.

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