ElemeNT- 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.
Before running (parameters information):
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.
May 2020- ElemeNT version 2 is here!
in this version, we added the option to run ElemNT 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), TFIIA response element (PMID: 28539359) and Pause button (PB, PMID: 18505835).
Please note! The color scheme of the displayed core promoter motifs was changed as compared to the original version.