FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses

Bioinformatics
Kathrin M SeibtTony Heitkam

Abstract

FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of ambiguities and substitutions. Our shading modules facilitate dotplot interpretation and motif identification by adding information on sequence annotations and sequence similarities. Combined with collage-like outputs, FlexiDot supports simultaneous visual screening of large sequence sets, enabling dotplot use for routine analyses. FlexiDot is implemented in Python 2.7. Software and documentation are freely available at http://github.com/molbio-dresden/flexidot. Supplementary data are available at Bioinformatics online.

Citations

Oct 15, 2019·The Plant Journal : for Cell and Molecular Biology·Kathrin M SeibtTony Heitkam
Jun 6, 2020·PloS One·Katherine A EasterlingHank W Bass
Jan 26, 2020·The Plant Journal : for Cell and Molecular Biology·Tony HeitkamThomas Schmidt
Oct 21, 2020·Genome Biology and Evolution·Isidoro FelicielloĐurđica Ugarković
Apr 21, 2021·Genome Research·Owen K SmithAaron F Straight
Sep 10, 2021·Virology Journal·Marta Kuźmińska-BajorRafał Kolenda

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