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.
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 separated either by a blank line or 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.
Default parameters include the following elements (and their corresponding cutoffs):
Mammalian Initiator (0.01), Drosophila Initiator (0.01), TATA box (0.01), MTE (0.01), DPE (0.01), Bridge (0.01), BRE upstream (0.05) and BRE downstream (0.5).
The PWMs used are described in following file.