CATSNAP: a user-friendly algorithm for determining the
conservation of protein variants reveals extensive parallelisms
in the evolution of alternative splicing

J 2023

CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing

TIMOFEYENKO, Kseniya, Dzmitry KANAVALAU, Panagiotis ALEXIOU, Maria KALYNA, Kamil RŮŽIČKA et. al.

Basic information

Original name

CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing

Authors

TIMOFEYENKO, Kseniya (112 Belarus, guarantor, belonging to the institution), Dzmitry KANAVALAU, Panagiotis ALEXIOU (300 Greece, belonging to the institution), Maria KALYNA and Kamil RŮŽIČKA

Edition

New Phytologist, Wiley, 2023, 0028-646X

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

20801 Environmental biotechnology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.400 in 2022

RIV identification code

RIV/00216224:14740/23:00132794

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1111/nph.18799

UT WoS

000959318600001

Keywords in English

alternative splicing; bioinformatics; determinism; isoforms; machine learning; molecular evolution; transcriptome

Abstract

V originále

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/.

Links

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

90140, large research infrastructures

Name: e-INFRA CZ

Citovat

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.

@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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