PROMO (prediction of transcription factor binding sites), ESSEM ...

PROMO is a program to predict transcription factor binding sites in DNA sequences. It can analyse one sequence or multiple related sequences. PROMO (prediction of transcription …

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FAQs about PROMO (prediction of transcription factor binding sites), ESSEM ... Coupon?

How can promo predict transcription factor binding sites?

Many binding sites for transcription factors have been experimentally identified and this information can be used to perform computational-based searches to characterise new gene regulatory regions. PROMO is a program to predict potential transcription factor binding sites in DNA sequences among those already experimentally identified. ...

How do I select a transcription factor?

step 1. SelectSpecies: select the species or group of species of interest. Also you can SelectFactors to restrict the prediction to a transcription factor set. step 2. or MultiSearchSites :input a set of sequences to search for binding sites that different sequences share. ViewMatrices :view details on weight matrices being used. See help . ...

What version of TRANSFAC does promo use?

PROMO is using version 8.3 of TRANSFAC. Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Nuñez, Javier Martínez, M.Mar Albà. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics, 18, 2, 333-334, 2002. ...

Why is transcription factor binding site recognition important?

Reliable transcription factor binding site (TFBS) recognition methods are essential for computer-assisted annotation of a large amount of genome sequence data. The paramount significance of this problem imposes a great challenge to bioinformaticians, resulting in a constantly increasing variety of approaches (1, 2). ...

How does a transcription factor interact with its binding sites?

A particular transcription factor can interact with its binding sites in a different fashion, thus making possible the situation when binding sites are present, for example, in the form of either direct or inverse repeats (25, 26) or conserved motifs with varying lengths of the spacer between them (27). ...

Is SP1 a transcription factor for gsdme promoter activity?

Next, to verify the direct DNA binding of Sp1 to its binding site, an EMSA assay was conducted. Anti-Sp1 antibody or Sp1 binding site mutation prevents the super-shifted complex formation observed in the presence of IgG (Fig. 1H). Thus, Sp1 is the transcription factor for GSDME promoter activity by binding its −36 ~ −28 site. ...