{"title":"用于非模式生物中快速差异基因表达分析的 DNA 蛋白质准图谱。","authors":"Kyle Christian L Santiago, Anish M S Shrestha","doi":"10.1186/s12859-024-05924-1","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Conventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning RNA-seq reads to a protein database, and demonstrated drastic improvements in speed, memory usage, and accuracy in identifying differentially expressed genes.</p><p><strong>Result: </strong>Here we report a further speed-up by replacing DNA-protein alignment by quasi-mapping, making our pipeline > 1000× faster than assembly-based approach, and still more accurate. We also compare quasi-mapping to other mapping techniques, and show that it is faster but at the cost of sensitivity.</p><p><strong>Conclusion: </strong>We provide a quick-and-dirty differential gene expression analysis pipeline for non-model organisms without a reference transcriptome, which directly quasi-maps RNA-seq reads to a reference protein database, avoiding computationally expensive transcriptome assembly.</p>","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"25 Suppl 2","pages":"335"},"PeriodicalIF":2.9000,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515663/pdf/","citationCount":"0","resultStr":"{\"title\":\"DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.\",\"authors\":\"Kyle Christian L Santiago, Anish M S Shrestha\",\"doi\":\"10.1186/s12859-024-05924-1\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Conventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning RNA-seq reads to a protein database, and demonstrated drastic improvements in speed, memory usage, and accuracy in identifying differentially expressed genes.</p><p><strong>Result: </strong>Here we report a further speed-up by replacing DNA-protein alignment by quasi-mapping, making our pipeline > 1000× faster than assembly-based approach, and still more accurate. We also compare quasi-mapping to other mapping techniques, and show that it is faster but at the cost of sensitivity.</p><p><strong>Conclusion: </strong>We provide a quick-and-dirty differential gene expression analysis pipeline for non-model organisms without a reference transcriptome, which directly quasi-maps RNA-seq reads to a reference protein database, avoiding computationally expensive transcriptome assembly.</p>\",\"PeriodicalId\":8958,\"journal\":{\"name\":\"BMC Bioinformatics\",\"volume\":\"25 Suppl 2\",\"pages\":\"335\"},\"PeriodicalIF\":2.9000,\"publicationDate\":\"2024-10-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515663/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s12859-024-05924-1\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12859-024-05924-1","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
摘要
背景：传统的非模式生物差异基因表达分析管道需要计算昂贵的转录组组装。我们最近提出了一种替代策略，即直接将 RNA-seq 读数与蛋白质数据库进行比对，结果表明，这种方法在速度、内存使用和识别差异表达基因的准确性方面都有大幅提高：结果：在这里，我们报告了用准映射代替 DNA 蛋白配准的进一步提速，使我们的管道比基于组装的方法快 1000 倍以上，而且更准确。我们还将类映射与其他映射技术进行了比较，结果表明，类映射速度更快，但灵敏度却有所降低：我们为没有参考转录组的非模式生物提供了一种快速简便的差异基因表达分析管道，它能直接将 RNA-seq 读数准映射到参考蛋白质数据库，避免了计算成本高昂的转录组组装。
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.
Background: Conventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning RNA-seq reads to a protein database, and demonstrated drastic improvements in speed, memory usage, and accuracy in identifying differentially expressed genes.
Result: Here we report a further speed-up by replacing DNA-protein alignment by quasi-mapping, making our pipeline > 1000× faster than assembly-based approach, and still more accurate. We also compare quasi-mapping to other mapping techniques, and show that it is faster but at the cost of sensitivity.
Conclusion: We provide a quick-and-dirty differential gene expression analysis pipeline for non-model organisms without a reference transcriptome, which directly quasi-maps RNA-seq reads to a reference protein database, avoiding computationally expensive transcriptome assembly.
期刊介绍：
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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