vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-24-95vavilov-4409Research ArticleЭВОЛЮЦИОННАЯ БИОЛОГИЯEVOLUTIONARY BIOLOGYOrthoweb: программный комплекс для эволюционного анализа генных сетейOrthoweb: a software package for evolutionary analysis of gene networkshttps://orcid.org/0000-0002-4369-356XИвановР. А.IvanovR. A.

Новосибирск

Novosibirsk

ivanovromanart@bionet.nsc.ruhttps://orcid.org/0000-0002-1102-0934МухинА. М.MukhinA. M.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-5711-7539КазанцевФ. В.KazantsevF. V.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-2724-4497МустафинЗ. С.MustafinZ. S.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-9738-1409АфонниковД. А.AfonnikovD. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-7754-8611МатушкинЮ. Г.MatushkinY. G.

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Novosibirsk

https://orcid.org/0000-0003-3138-381XЛашинС. А.LashinS. A.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian FederationНовосибирский национальный исследовательский государственный университетРоссияNovosibirsk State UniversityRussian Federation202425012025288874881Copyright © Иванов Р.А., Мухин А.М., Казанцев Ф.В., Мустафин З.С., Афонников Д.А., Матушкин Ю.Г., Лашин С.А., 20252025Иванов Р.А., Мухин А.М., Казанцев Ф.В., Мустафин З.С., Афонников Д.А., Матушкин Ю.Г., Лашин С.А.Ivanov R.A., Mukhin A.M., Kazantsev F.V., Mustafin Z.S., Afonnikov D.A., Matushkin Y.G., Lashin S.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4409

В данной статье описывается Orthoweb (https://orthoweb.sysbio.cytogen.ru/) – программный ком­плекс, разработанный для вычисления эволюционных индексов, включая филостратиграфические индексы и индексы дивергенции (Ka/Ks) как отдельных генов, так и генных сетей. Индекс филостратиграфического возрас­та (PAI) позволяет оценить эволюционную стадию появления гена (при этом косвенно оценив приблизительное время его возникновения – так называемый эволюционный возраст) на основе анализа ортологичных генов у близкородственных и дальнородственных таксонов. Кроме того, Orthoweb поддерживает расчет индексов воз­раста транскриптома (TAI) и дивергенции транскриптома (TDI). Эти индексы важны для понимания динамики экспрессии генов и ее последствий для развития и адаптации организмов. Orthoweb содержит также дополни­тельные аналитические функции, такие как возможность анализа терминов Gene Ontology (GO), что позволяет проводить функциональное обогащение и связывать эволюционное происхождение генов с биологическими процессами. Помимо этого, доступна возможность анализа обогащения по однонуклеотидным полиморфизмам (SNP), который помогает исследовать эволюционное значение генетических вариантов в конкретных ге­номных регионах. Одной из ключевых особенностей Orthoweb является интеграция перечисленных индексов с анализом генетических сетей. Программный пакет предлагает расширенные средства визуализации, такие как картирование генетических сетей и графическое представление распределения филостратиграфических индексов элементов сетей, что облегчает интуитивную интерпретацию сложных эволюционных связей. Для упрощения рабочих процессов в Orthoweb включена база данных с предварительно рассчитанными индекса­ми для множества таксонов, доступная через API. Эта функция позволяет эффективно получать готовые данные по филостратиграфическим индексам и индексам дивергенции, значительно сокращая время вычислений.

This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene’s emergence (and thus indirectly the approximate time of its origin, known as “evolutionary age”) to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the transcriptome age index (TAI) and the transcriptome divergence index (TDI). These indices are important for understanding the dynamics of gene expression and its impact on the development and adaptation of organisms. Orthoweb also includes optional analytical features, such as the ability to explore Gene Ontology (GO) terms associated with genes, facilitating functional enrichment analyses that link evolutionary origins of genes to biological processes. Furthermore, it offers tools for SNP enrichment analysis, enabling the users to assess the evolutionary significance of genetic variants within specific genomic regions. A key feature of Orthoweb is its ability to integrate these indices with gene network analysis. The software offers advanced visualization tools, such as gene network mapping and graphical representations of phylostratigraphic index distributions of network elements, ensur­ing intuitive interpretation of complex evolutionary relationships. To further streamline research workflows, Orthoweb includes a database of pre-calculated indices for numerous taxa, accessible via an application programming inter­face (API). This feature allows the users to retrieve pre-computed phylostratigraphic and divergence data efficiently, significantly reducing computational time and effort.

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The authors declare that there are no conflicts of interest present.