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README.md

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)