DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms

Autor:	Kyle Christian L. Santiago, Anish M. S. Shrestha
Jazyk:	angličtina
Rok vydání:	2024
Předmět:	Quasi-mapping DNA-protein alignment RNA-seq Non-model organism Differential gene expression analysis Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Zdroj:	BMC Bioinformatics, Vol 25, Iss S2, Pp 1-15 (2024)
Druh dokumentu:	article
ISSN:	1471-2105
DOI:	10.1186/s12859-024-05924-1
Popis:	Abstract 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.
Databáze:	Directory of Open Access Journals
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