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

• Published in: BMC bioinformatics Vol. 25; no. Suppl 2; pp. 335 - 15
• Main Authors: Santiago, Kyle Christian L, Shrestha, Anish M S
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 24-10-2024; BioMed Central; BMC
• Subjects: Analysis; Assembly; Computational biology; Deoxyribonucleic acid; Differential gene expression analysis; DNA; DNA - genetics; DNA - metabolism; DNA-protein alignment; Gene expression; Gene Expression Profiling - methods; Gene mapping; Genes; Mapping; Medical care, Cost of; Methods; Non-model organism; Organisms; Peptide mapping; Proteins; Proteins - genetics; Proteins - metabolism; Quasi-mapping; Ribonucleic acid; RNA; RNA sequencing; RNA-seq; Sequence Alignment - methods; Software; Transcriptome - genetics; Transcriptomes; Philippines; Differential gene expression analysis; DNA-protein alignment; Quasi-mapping; RNA-seq; Non-model organism
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05924-1

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.
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.
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.