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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) for 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 ElemeNT 2023 is available for download at GitHub using the link here.
ElemeNT version 2023 was released on August 2023
Enhancements included in this release:
The ElemeNT algorithm now uses as background the provided GC content.
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)
Please note! The color scheme of the displayed core promoter motifs was changed as compared to the original version.
ElemeNT parameters (recommended to review before running)
Sequence–
The input sequence should be provided either as plain text or in FASTA format. Multiple sequences should be provided in FASTA format (sequence description line starts with ‘>’). Each analyzed sequence can contain up to 1000bp.
Elements and corresponding cutoffs–
The elements for search can be chosen by checking the check box to the left of the desired element. The recommended cutoff score value can be changed as needed. 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 by ElemeNT are described in ElemeNT_PWM_V2023.xlsx
differently, we have also included the corresponding values for few species.
| Fly, dm6 (42.03 %GC) | Human, hg38 (40.4 %GC) | Worm, ce6 (35.43 %GC) | ||||||
|---|---|---|---|---|---|---|---|---|
| recommended | min | max | min | max | min | max | ||
| BBCABW | 3.6 | -∞ | 7.24 | -∞ | 7.39 | -∞ | 7.91 | |
| BREd | 4.2 | -9.93 | 5.02 | -10.02 | 5.13 | -10.37 | 5.97 | |
| BREu | 5.8 | -28.67 | 11.97 | -28.95 | 12.37 | -29.76 | 13.7 | |
| bridge1 | 0.78 | -3.84 | 3.54 | -4.04 | 3.82 | -4.62 | 4.77 | |
| bridge2 | 0.78 | -12.61 | 4.84 | -12.58 | 4.88 | -12.43 | 5.02 | |
| dInr | 2.3 | -∞ | 9.05 | -∞ | 9.1 | -∞ | 9.32 | |
| DPE | 0.7 | -∞ | 7.62 | -∞ | 7.77 | -∞ | 8.29 | |
| dTCT | 9.5 | -31.64 | 12.03 | -31.76 | 11.91 | -32.36 | 11.64 | |
| GAGA | 6.7 | -42.04 | 13.56 | -42.15 | 13.74 | -42.39 | 14.57 | |
| hInr | 0.7 | -∞ | 8.17 | -∞ | 8.37 | -∞ | 9.09 | |
| hTCT | 6 | -24.74 | 9.33 | -24.92 | 9.44 | -25.43 | 9.85 | |
| Motif 1 | 11 | -101.33 | 19.39 | -101.48 | 19.63 | -101.83 | 20.49 | |
| MTE | 8.5 | -36.65 | 17.23 | -37.04 | 17.82 | -38.12 | 19.79 | |
| PB | 7.6 | -40.72 | 12.09 | -40.8 | 12.39 | -41 | 13.41 | |
| TATA | 6 | -∞ | 11.08 | -∞ | 10.86 | -∞ | 10.24 | |
| XCPE 1 | 4 | -49.63 | 17.72 | -49.93 | 18.19 | -50.78 | 19.78 | |
| XCPE 2 | 6 | -45.01 | 17.96 | -45.45 | 18.39 | -46.72 | 19.86 | |