改善了对参考蛋白质组的正规蛋白质的选择
Giuseppe Insana1, Maria J Martin1, William R Pearson2
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
NAR genomics and bioinformatics
|June 12, 2024
概括
在更高的真核生物中,UniProt的正规蛋白质序列可能不一致. ortho2tree管道通过识别生物学相关的异型来改善规范性赋值,提高了蛋白质注释的准确性.
科学领域:
- 生物信息学是一种生物信息学.
- 蛋白质组学是指蛋白质组学.
- 基因组学就是基因组学.
背景情况:
- UniProt 规范性蛋白质序列对于研究至关重要,但由于异型选择,在较高的真核生物中可能不一致.
- 在未经审查的蛋白质数据库中,最长的序列通常被选择为正规序列,从而导致高度相似的正统序列中生物学上不太可能存在长度变化.
研究的目的:
- 开发和验证 ortho2tree 管道,以改善正规蛋白质序列分配.
- 为了解决在较高的真核生物中由替代拼接产生的正规蛋白质选择中的不一致性.
主要方法:
- ortho2tree管道分析了正统的蛋白质序列,建立了多个对齐,并构建了家族遗传树来识别具有相似长度的异型.
- 它检查了来自UniProt参考蛋白质的规范和异形序列,专注于哺乳动物.
主要成果:
- ortho2tree在UniProtKB发布2023_01.01中提出了7804项规范性变更,并确认了53,434项规范性变更.
- 管道的异形选择导致差距分布与细菌和酵母菌的差距分布相似,这表明生物准确性得到了改善.
- ortho2tree与MANE (Eukaryotes系统匹配注释) 标准达成高度一致,对拟议的变化达成82%的同意,对确认的正规性达成92%的同意.
结论:
- ortho2tree管道为分配正规蛋白质序列提供了更准确的方法,特别是在脊椎动物和植物中.
- 改进的法典赋值提高了蛋白质相似性搜索,功能注释和结构分析的可靠性.
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