Elements Navigation Tool

ElemeNT is an interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language.

The input sequence is searched against the position weight matrices (PWMs) of biologically-functional core promoter elements in order to generate the corresponding probability score. 

Only sequence motifs with probability scores above the specified cutoffs are displayed in the output table.

Please note- the results for each element are displayed separately, and are ordered by score values.

Command line version of the ElemeNT algorithm are available upon request.

For further information, please contact us.

Before running (parameters information):

Sequence

The allowed sequence formats are either plain text or FASTA. Multiple sequences can be run during the same instance, if they are in FASTA format (lines starting with ‘>’). Each analyzed sequence can contain up to 1000bp.

Elements and corresponding cutoffs

Check the specific elements you would like to search within the input sequence. For each element, a cutoff between 0 and 1 should be specified, with 1 being the highest possible match and 0 the least possible. Only elements with PWM score equal to, or higher than, the cutoff will be displayed under the ‘results’ table. Leaving the cutoff without a value is equal to inserting ‘0’ value. 

 The PWMs used are described in the following file.

 

ElemeNT version 2 was released on May 2020

Enhancements included in this release:

It is now possible to run ElemeNT on the reverse complement sequence as well. 

The following motifs were added:

  • GAGA (CISBP motif M5247, version 1.02)
  • Ohler Motif 1 (PMID: 12537576)
  • BBCABW Initiator (PMID: 28108474)
  • Pause button (PB, PMID: 18505835)
  • TFIIA response element (PMID: 28539359)

Please note! The color scheme of the displayed core promoter motifs was changed as compared to the original version.