Analyze any DNA sequence for site enrichment (GTRD) (workflow)

Workflow title

Analyze any DNA sequence for site enrichment (GTRD)

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to search for enriched transcription factor binding sites, TFBSs, in any input DNA sequence as compared to a background DNA sequence. With this workflow you can analyze sequences of any species and any genomic region.

The input Yes and No sequences are subjected to ‘Site search on track’ method, using the default profile from GTRD database ‘moderate threshold’.   The results of the site search on track are then subjected to ‘Site search result optimization’. 

The results folder consists of several tables and tracks. Summary table gives the TFBSs enriched in the Yes set as compared with the No set. The optimized tracks present those TFBSs that are over-represented in the Yes sequences versus the No sequences. Scores of the putative sites are optimized by the algorithm.

Transcription factors table aim at showing transcription factors linked to the identified site models (matrices). These are potential candidate regulators of genes in the input Yes set. They are supposed to regulate transcription of Yes-genes via the identified enriched TFBSs.

 

 

Parameters

Input Yes sequence set

Select Yes sequence set

Input No sequence set

Select No sequence set

Profile

Select Profile

Results folder

Select Results folder