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SynoR :: Genome Miner for Synonymous Regulation

Bps, but not more than. Note: The minimal distance is 3 bps, the maximal is 1000 bps.). Format: name count strand ). Fix the order of TFBS. List of available TFBS. Return to previously submitted request. NCBI DCODE.org Comparative Genomics Developments.

http://synor.dcode.org/

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SynoR :: Genome Miner for Synonymous Regulation | synor.dcode.org Reviews
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Bps, but not more than. Note: The minimal distance is 3 bps, the maximal is 1000 bps.). Format: name count strand ). Fix the order of TFBS. List of available TFBS. Return to previously submitted request. NCBI DCODE.org Comparative Genomics Developments.
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SynoR :: Genome Miner for Synonymous Regulation | synor.dcode.org Reviews

https://synor.dcode.org

Bps, but not more than. Note: The minimal distance is 3 bps, the maximal is 1000 bps.). Format: name count strand ). Fix the order of TFBS. List of available TFBS. Return to previously submitted request. NCBI DCODE.org Comparative Genomics Developments.

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1

Citing SynoR

http://synor.dcode.org/citing.php

If you find SynoR. Useful in your research, please cite it as:. I Ovcharenko and M.A. Nobrega. Identifying synonymous regulatory elements in vertebrate genomes. 33, W403-7, (2005) [ PDF.

2

Synor :: Details

http://synor.dcode.org/details.php

3

SynoR :: List of available TFBS

http://synor.dcode.org/listTFBS.php

List of available TFBS. Total number of TFBS: 584.

4

SynoR :: Instructions

http://synor.dcode.org/instruct.php

Search for a pair of GATA1 sites. Search for a pair of GATA1 sites on the same strand. Search for GATA1 site on the positive strand followed by 2 HNF4 sites on the negative strand HNF4 2. Sometimes there is more than 1 TFBS matrix per TF in the TRANSFAC database utilized by SynoR. For example, there are 5 TRANSFAC matrices for the SP1 TFBS (SP1 01, SP1 Q6, SP1 Q6 01, SP1 Q4 01, SP1 Q2 01). In such cases, the SP1 2. Input specification will be searching for a pair of ANY. Select the Fix the order of TFBS.

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dire.dcode.org dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

http://dire.dcode.org/cite.php

Return to submitted job. If you find the results useful for your research, please cite DiRE as. Gotea, V. and I. Ovcharenko ( 2008. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Research. Doi:10.1093/nar/gkn300 [ Abstract. NCBI DCODE.org Comparative Genomics Developments ( www.dcode.org.

dire.dcode.org dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

http://dire.dcode.org/index.php?id=example

The requested ID is not valid. Please let us know ( dcode@ncbi.nlm.nih.gov.

dire.dcode.org dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

http://dire.dcode.org/return.php

Return to submitted job. Please enter a 16-digit request ID. To return to your previously submitted job:. NCBI DCODE.org Comparative Genomics Developments ( www.dcode.org.

dire.dcode.org dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

http://dire.dcode.org/details.php

Return to submitted job. Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors, and silencers. We developed a web server called DiRE. Lements, based on the Enhancer Identification (EI) method. Allows users to start their analysis with raw microarray expression data. Continue to: screen shots.

dire.dcode.org dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

http://dire.dcode.org/screenshots.php

Return to submitted job. You'll see this screen while DiRE is running. Note the job ID at the top, you can use it later to return to your query. It can take up to 30 minutes for a job to complete, depending on the number of signal and background genes supplied. After a successful completion of your query, DiRE will display a results page, divided into four sections as follows:. If you didn't copy this 16-digit number from the running screen, do it now! In a nutshell, here is what you were looking for!

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SynoR :: Genome Miner for Synonymous Regulation

Bps, but not more than. Note: The minimal distance is 3 bps, the maximal is 1000 bps.). Format: name count strand ). Fix the order of TFBS. List of available TFBS. Return to previously submitted request. NCBI DCODE.org Comparative Genomics Developments.

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