What it does
This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):
| Column | Description |
| 1 | Sequence identifier (first word of FASTA header) |
| 2 | Promoter position, e.g. 600 |
| 3 | Promoter score, e.g. 1.063 |
| 4 | Promoter likelihood, e.g. Highly likely prediction |
The scores are classified very simply as follows:
| Score | Description |
| below 0.5 | ignored |
| 0.5 - 0.8 | Marginal prediction |
| 0.8 - 1.0 | Medium likely prediction |
| above 1.0 | Highly likely prediction |
Internally the input FASTA file is divided into parts (to allow multiple processors to be used), and the raw output is reformatted into this tabular layout suitable for downstream analysis within Galaxy.
References
If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:
Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 https://doi.org/10.7717/peerj.167
Steen Knudsen (1999). Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics, 15:356-61. https://doi.org/10.1093/bioinformatics/15.5.356
See also http://www.cbs.dtu.dk/services/Promoter/output.php
This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp