Sequrutinator：仔细检查大型蛋白质超家族序列数据集，以识别和消除无功能同源物。

IF 12.3 1区生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2024-08-26 DOI:10.1186/s13059-024-03371-y

Agustín Amalfitano, Nicolás Stocchi, Hugo Marcelo Atencio, Fernando Villarreal, Arjen Ten Have

{"title":"Sequrutinator：仔细检查大型蛋白质超家族序列数据集，以识别和消除无功能同源物。","authors":"Agustín Amalfitano, Nicolás Stocchi, Hugo Marcelo Atencio, Fernando Villarreal, Arjen Ten Have","doi":"10.1186/s13059-024-03371-y","DOIUrl":null,"url":null,"abstract":"Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda's recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"25 1","pages":"230"},"PeriodicalIF":12.3000,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346255/pdf/","citationCount":"0","resultStr":"{\"title\":\"Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues.\",\"authors\":\"Agustín Amalfitano, Nicolás Stocchi, Hugo Marcelo Atencio, Fernando Villarreal, Arjen Ten Have\",\"doi\":\"10.1186/s13059-024-03371-y\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda's recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.\",\"PeriodicalId\":48922,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"25 1\",\"pages\":\"230\"},\"PeriodicalIF\":12.3000,\"publicationDate\":\"2024-08-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346255/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-024-03371-y\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-024-03371-y","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}

引用次数: 0

摘要

Seqrutinator 是一个客观、灵活的管道，可从复杂的真核生物蛋白质超家族中移除存在测序和/或基因模型错误的序列以及来自假基因的序列。在主要超家族 BAHD、CYP 和 UGT 上测试 Seqrutinator，只移除了 1.94% 的 SwissProt 条目、14% 的模式植物拟南芥条目，但移除了 80% 的太田松近期完整蛋白质组条目。将 Seqrutinator 应用于从 16 个植物蛋白质组中获得的粗 BAHDomes、CYPomes 和 UGTomes，结果显示旁系物的数量趋于一致。应用 Seqrutinator 后，MSA、系统发育，特别是功能聚类得到了显著改善，显示出良好的性能。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues.

Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda's recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

25.50

自引率

3.30%

发文量

审稿时长

14 weeks

期刊介绍： Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.