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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F23%3A00575856" target="_blank" >RIV/61389030:_____/23:00575856 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14740/23:00132794

Result on the web

<a href="https://doi.org/10.1111/nph.18799" target="_blank" >https://doi.org/10.1111/nph.18799</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/nph.18799" target="_blank" >10.1111/nph.18799</a>

Result language

angličtina

Original language name

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

Original language description

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/.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

20801 - Environmental biotechnology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

New Phytologist

ISSN

0028-646X

e-ISSN

1469-8137

Volume of the periodical

238

Issue of the periodical within the volume

4

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

1722-1732

UT code for WoS article

000959318600001

EID of the result in the Scopus database

2-s2.0-85149905020