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Интеллектуальная Система Тематического Исследования НАукометрических данных |
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OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteinsстатья
Статья опубликована в высокорейтинговом журнале
Статья опубликована в журнале из списка Web of Science и/или ScopusДата последнего поиска статьи во внешних источниках: 1 июня 2022 г.
- Авторы: Ilnitskiy Ivan S., Zharikova Anastasia A., Mironov Andrey A.
- Журнал: Nucleic Acids Research
- Том: 2022
- Год издания: 2022
- Издательство: Oxford University Press
- Местоположение издательства: United Kingdom
- Первая страница: gkac385
- Последняя страница: gkac385
- Номер статьи: gkac385
- DOI: 10.1093/nar/gkac385
- Аннотация: Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the evolutionary landscape of related proteins. Here, we present OrthoQuantum, a web server that allows for time-efficient analysis and visualization of phylogenetic profiles of any set of eukaryotic proteins. It is a simple-to-use tool capable of searching large input sets of proteins. Using data from open source databases of orthologous sequences in a wide range of taxonomic groups, it enables users to assess coupled evolutionary patterns and helps define lineage-specific innovations. The web interface allows to perform queries with gene names and UniProt identifiers in different phylogenetic clades and supplement presence with an additional BLAST search. The conservation patterns of proteins are coded as binary vectors, i.e., strings that encode the presence or absence of orthologous proteins in other genomes. These strings are used to calculate top-scoring correlation pairs needed for finding co-inherited proteins which are simultaneously present or simultaneously absent in specific lineages. Profiles are visualized in combination with phylogenetic trees in a JavaScript-based interface. The OrthoQuantum v1.0 web server is freely available at http://orthoq.bioinf.fbb.msu.ru along with documentation and tutorial.
- Добавил в систему: Ильницкий Иван Сергеевич