TRviz: a Python library for decomposing and visualizing tandem repeat sequences

Jonghun Park; Eli Kaufman; Paul N Valdmanis; Vineet Bafna

doi:10.1093/bioadv/vbad058

TRviz: a Python library for decomposing and visualizing tandem repeat sequences

Bioinform Adv. 2023 Apr 26;3(1):vbad058. doi: 10.1093/bioadv/vbad058. eCollection 2023.

Authors

Jonghun Park¹, Eli Kaufman², Paul N Valdmanis², Vineet Bafna¹

Affiliations

¹ Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
² Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA.

Abstract

Summary: TRviz is an open-source Python library for decomposing, encoding, aligning and visualizing tandem repeat (TR) sequences. TRviz takes a collection of alleles (TR containing sequences) and one or more motifs as input and generates a plot showing the motif composition of the TR sequences.

Availability and implementation: TRviz is an open-source Python library and freely available at https://github.com/Jong-hun-Park/trviz. Detailed documentation is available at https://trviz.readthedocs.io.

Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Grants and funding

R01 GM114362/GM/NIGMS NIH HHS/United States