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Citations per year

Number of citations per year for the bioinformatics software tool Matcompare

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This map represents all the scientific publications referring to Matcompare per scientific context
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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

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

[…] cluster. The background sequence file was generated by using the computer program ‘’ in the Bioinformatics CPAN Perl module of InSilicoSpectro-Databanks version 0.0.43. The Matcompare program in the CREAD package was used to compute the similarity between the identified DME motif and those in the TRANSFAC, JASPAR and ENCODE databases [–]. The Position Frequency Matrices […]


Regulatory elements of Caenorhabditis elegans ribosomal protein genes

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

[…] were also found to be similar to characterized TF binding sites from C. elegans, human, Drosophila, and yeast (Figure ). We used three motif-motif comparison methods to find the similarities (STAMP, Matcompare, and TESS), and found that they produced non-overlapping results. This finding indicates that in spite of the multitude of available methods, accurate and meaningful motif-motif similarity […]


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

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

[…] To quantify the similarity in binding preferences between MarA variants, we used the program MatCompare to calculate the Kullback-Leiber Divergence (KLD) between the inferred sequence logos . All pair-wise KLD values are reported in . The relative affinity () of a given binding model to all D […]


A Systems Biology Approach to Transcription Factor Binding Site Prediction

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

[…] against which we assessed the statistical significance of the de novo identified motifs from the original set. Motifs in the 95th percentile (p≤0.05) are said to be statistically significant.We used matcompare with a similarity cutoff of 1.0 bit for motif comparison. DME was used to discover enriched motifs of length 6, 8, and 10. Similar top motifs were merged using uniqmotifs . GibbsModule w […]


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

Nucleic Acids Res
PMCID: 2790884
PMID: 19767611
DOI: 10.1093/nar/gkp747

[…] n 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 o […]


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

Nucleic Acids Res
PMCID: 2724271
PMID: 19491311
DOI: 10.1093/nar/gkp425

[…] over-represented motifs compared to a suitable background set (see ‘Materials and Methods’ section). These motifs were compared to the TRANSFAC and Jaspar collections of PWMs using the CREAD program MATCOMPARE. Comparison was estimated using a divergence score in the range of 0 to 1, where a divergence of 0 indicates the motif predicted de-novo is identical to a PWM. HIF-1 PWMs were matched best […]

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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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