Analyze any DNA sequence (GTRD) (workflow)

Workflow title

Analyze any DNA sequence (GTRD)

Provider

geneXplain GmbH

Workflow overview

Description

This workflow is designed to search for putative transcription factor binding sites, TFBS, in any input DNA sequence in EMBL, Fasta or Genbank formats. Using this workflow you can analyze DNA sequences of any species and of any genomic regions.

 

The input sequence is subjected to ‘Site search on track’ method using the profile from the GTRD database called moderate threshold. The output sites are then subjected to the method ‘Site search summary’, which generates summary on the site search result. 

The results folder consists of a summary table and a track with sites. The track shows TFBSs that are found in the input sequences. 

 

Each row in the track file corresponds to one resulting TFBS and includes sequence names, site positions (the columns From and To), site Length and Strand, score calculated by the algorithm and a site model (here, GTRD matrix). This table can be exported as a track in several different formats including intervals, bed, wig and more. DNA sequences can be exported in multi-FASTA format.

 

The table Summary gives the site density per thousand bp for each matrix in the input sequence. For each row, the column Site density per 1000bp shows the number of matches normalized per 1000 bp length for the sequences in the input set.  TFBSs can be visualized in the genome browser.

 

 

Parameters

Input sequence

Select Yes sequence set

Profile

Select Profile

Results folder

Select Results folder