| TIMOFEYENKO, Kseniya, Dzmitry KANAVALAU, Panagiotis ALEXIOU, Maria KALYNA and Kamil RŮŽIČKA. CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. New Phytologist. Wiley, 2023, vol. 238, No 4, p. 1722-1732. ISSN 0028-646X. Available from: https://dx.doi.org/10.1111/nph.18799. |
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@article{2356497,
author = {Timofeyenko, Kseniya and Kanavalau, Dzmitry and Alexiou, Panagiotis and Kalyna, Maria and Růžička, Kamil},
article_number = {4},
doi = {http://dx.doi.org/10.1111/nph.18799},
keywords = {alternative splicing; bioinformatics; determinism; isoforms; machine learning; molecular evolution; transcriptome},
language = {eng},
issn = {0028-646X},
journal = {New Phytologist},
title = {CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing},
url = {https://doi.org/10.1111/nph.18799},
volume = {238},
year = {2023}
}
TY - JOUR
ID - 2356497
AU - Timofeyenko, Kseniya - Kanavalau, Dzmitry - Alexiou, Panagiotis - Kalyna, Maria - Růžička, Kamil
PY - 2023
TI - CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing
JF - New Phytologist
VL - 238
IS - 4
SP - 1722-1732
EP - 1722-1732
PB - Wiley
SN - 0028646X
KW - alternative splicing
KW - bioinformatics
KW - determinism
KW - isoforms
KW - machine learning
KW - molecular evolution
KW - transcriptome
UR - https://doi.org/10.1111/nph.18799
N2 - Understanding the evolutionary conservation of complex eukaryotic transcriptomes significantly illuminates the physiological relevance of alternative splicing (AS). Examining the evolutionary depth of a given AS event with ordinary homology searches is generally challenging and time-consuming. Here, we present Catsnap, an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by AS. It employs a machine learning approach following a database search with the provided pair of protein sequences. We used the Catsnap algorithm for analyzing the conservation of emerging experimentally characterized alternative proteins from plants and animals. Indeed, most of them are conserved among other species. Catsnap can detect the conserved functional protein isoforms regardless of the AS type by which they are generated. Notably, we found that while the primary amino acid sequence is maintained, the type of AS determining the inclusion or exclusion of protein regions varies throughout plant phylogenetic lineages in these proteins. We also document that this phenomenon is less seen among animals. In sum, our algorithm highlights the presence of unexpectedly frequent hotspots where protein isoforms recurrently arise to carry physiologically relevant functions. The user web interface is available at https://catsnap.cesnet.cz/.
ER -
TIMOFEYENKO, Kseniya, Dzmitry KANAVALAU, Panagiotis ALEXIOU, Maria KALYNA and Kamil RŮŽIČKA. CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. \textit{New Phytologist}. Wiley, 2023, vol.~238, No~4, p.~1722-1732. ISSN~0028-646X. Available from: https://dx.doi.org/10.1111/nph.18799.
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