Tandem Repeat Annotation Library¶
TRAL makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.
A working TRAL installation consists of several parts:
The TRAL python package
External tools and repeat detectors.
TRAL configuration files and supporting data.
TRAL itself requires Python3 and should run on all platforms. However, many external tools require linux. The full TRAL pipeline has been tested on ubuntu.
The easiest way to get started on ubuntu is to use the easy setup system. This automatically installs TRAL and all external tools.
We also provide a docker <https://github.com/acg-team/tral/packages> image with TRAL and all its third party software set up.
Alternately, follow these steps to install each part:
Finally, adapt the configuration files.
If you have trouble installing TRAL on your system, consider using the containerized install .
Run and parse de novo repeat detection software.
Background about tandem repeat characteristics in TRAL
Annotate tandem repeats from sequence domain models.
Perform statistical significance test of tandem repeats.
Perform overlap filtering of redundant tandem repeat annotations.
Use GC3Pie to annotate your large sequence dataset (toy example)
Find instances of a particular repeat in a sequence database.
How to cite us¶
E Schaper, A Korsunsky, J Pecerska, A Messina, R Murri, H Stockinger, S Zoller, I Xenarios, and M Anisimova (2015). TRAL: Tandem Repeat Annotation Library. Bioinformatics. DOI: 10.1093/bioinformatics/btv306
More on contributors and the background of this project.