Priming Site Predictor of Transcript Sequences
Priming Site Predictor which uses a seed-and-extension algorithm (RIblast:https://github.com/fukunagatsu/RIblast) to Predict Priming Sites of oligo dT primers in target sequences. Further, Binding Energies are calculated and classified with a threshold value. Additionally, the binding sites are associated with Binding Probabilities and stored in a GTF File for further processes.
Version
Version 0.1.0 (2022/11/15)
Acknowledgements
We used the Riblast algorithm created by Tsukasa Fukunaga (https://github.com/fukunagatsu ).
Usage
Example
Command and Options
Output file format
License
This software is released under the MIT License, see LICENSE.txt.
Changelogs
2022/11/15 Version 0.1.0 was released.
Contributors
Max Bär, Sophie Schnider, Robin Christen (University of Basel)
Reference
Tsukasa Fukunaga and Michiaki Hamada. "RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach." btx287, Bioinformatics (2017)