LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.

IF 3.2 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Genome Biology and Evolution Pub Date : 2024-11-01 DOI:10.1093/gbe/evae231

Łukasz F Sobala

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引用次数: 0

Abstract

The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.

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LukProt：真核生物预测蛋白质数据库，用于研究动物起源。

动物的起源和早期进化是一个有许多悬而未决问题的课题。试图回答这些问题的研究人员面临的一个问题是缺乏一个包含非两栖动物序列的综合数据库。可公开获得的数据很多，但很分散，而且往往没有适当的元数据。本文介绍的新数据库 LukProt 就是为解决这一问题而进行的尝试。该数据库包含主要从基因组、转录组和元基因组研究中获得的蛋白质序列，是 EukProt 的扩展（Richter 等人，2022 年，《同行社区期刊》，2，e56）。LukProt 采用了 EukProt 的命名规则，并包含了另外 216 种动物的数据。该数据库与适合研究早期动物进化的分类分组（taxogroup）方案相关联。数据库的小更新包括物种添加或元数据更正，大更新将使 LukProt 与 EukProt 的每个新版本同步，发布的数据将永久保存在 Zenodo（https://doi.org/10.5281/zenodo.7089120）上。用于搜索数据库的 BLAST 服务器可在 https://lukprot.hirszfeld.pl/ 上使用。我们邀请用户参与 LukProt 的维护和修正。由于无需本地下载即可进行搜索，该数据库不仅对进化生物学家，而且对更广泛的科学界都是一种便利的资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY

CiteScore

5.80

自引率

6.10%

发文量

169

审稿时长

1 months

期刊介绍： About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.