Analyze any DNA sequence for site enrichment

This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  

As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.

At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The profile can be selected depending upon the input sequence collection.

In the next step the results of Site search on track for Yes and No sequences are used as input to Site search result optimization. This analysis generates a table containing TFBS enriched in the Yes set in comparison with the No set. In the output, matrices with an enrichment ratio (Yes/No ratio) >1 are shown.  

Next, the list of PWMs is converted into a table of transcription factors. Two tables are produced, one with Ensembl IDs and one with Entrez IDs.
Finally, both tables with transcription factors are annotated with additional information, gene descriptions and gene symbols.

The output is a new folder with several tables, including a summary of the enriched TFBSs, genomic tracks of the Yes and No sequence collection and TFBSs, as well as the tables with transcription factors potentially regulating the sequences in the Yes set.

Tracks can be further used for visualizing input sequences, and TFBSs on chromosomes (available for human, mouse and rat sequences).

What is the geneXplain type?

The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual workflows (geneXplain type), or Bricks, are unified under a standardized interface.
To run the workflows you just need to register for a free account here:

http://www.genexplain.com/genexplain-platform-registration

You get a password from BioStore to login the platform. It is open for everyone.

After clicking the workflow link (bottom) you can immediately enter the platform and execute the workflow via simple drag and drop of uploaded data files in your project.

Workflow_Analyze any DNA sequence for site enrichment

See also

•     http://wiki.biouml.org/index.php/Category:GeneXplain_analyses
•     http://wiki.biouml.org/index.php/Category:GeneXplain_workflows