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MatDefine specifications


Unique identifier OMICS_26748
Name MatDefine
Interface Web user interface
Restrictions to use License purchase required
Input data A sequence or a matrix.
Input format EMBL,GenBank,FASTA,IG
Output data A protocol detailing each step of the matrix generation, and the weight matrix.
Computer skills Basic
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes


  • person_outline GGA Team <>

Additional information

MatDefine is part of GEMS Launcher, which is part of Genomatix Software Suite.

MatDefine citations


STAT1 Dependent Signal Integration between IFNγ and TLR4 in Vascular Cells Reflect Pro Atherogenic Responses in Human Atherosclerosis

PMCID: 4257532
PMID: 25478796
DOI: 10.1371/journal.pone.0113318

[…] a list of over-represented transcription factor binding sites together with occurrences of each site and a matrix similarity score. occurrences having the score of at least 0.8 were fed into matdefine (genomatix software package) to create a highly conserved matrix for each transcription factor binding site. the settings were as follows: tuple size – 8; no. of sequences containing tuple […]


Genome wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription

PMCID: 3082894
PMID: 21177654
DOI: 10.1093/nar/gkq1301

[…] performed with a position-specific scoring matrix (pssm) built using 347 experimentally validated binding sites (). matrix generation and scan of sequences were done using the genomatix suite, with matdefine and matinspector programs (), respectively. significant overrepresentation of sbs in bidirectional promoters was evaluated using the khi2 test for two proportions, with alpha = 0.05 and 1 […]


Proteomic Analysis of Native Hepatocyte Nuclear Factor 4α (HNF4α) Isoforms, Phosphorylation Status, and Interactive Cofactors*

PMCID: 3013027
PMID: 21047794
DOI: 10.1074/jbc.M110.154732

[…] similar sequences were extracted from the top 1000 sequences with the highest signal rates in the chip-seq data using the matinspector search tool (). the final motifs were generated with the matdefine tool () using the frequency of the extracted sequences from matinspector., the duplex constructs for each small interfering rna (sirna) targeting hnf4α mrna, i.e. 4α-(i) and 4α-(ii), along […]


Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l1 l2 Regularization and Data Reduction

PMCID: 2905945
PMID: 20652058
DOI: 10.1155/2010/878709

[…] and generated a dataset containing the promoters of the genes coding for the mrnas spotted on the chip. the hre matrix has been obtained from 69 experimental validated human hre sequences [] with matdefine tool (genomatix software gmbh). hre consensus elements [(g|c|a|t) (c|g|t|a) (g|c|a|t) (t|g|c|a) (a|g) (cgtg) (c|g|t|a) (g|c|a|t) (g|c|t|a) (c|g|t|a)] were searched in the promoter sequences […]

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