方法对比

	序列比对	Single-cell RNA-seq analysis
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	1970 (global alignment); 1981 (local alignment)	2009 (first scRNA-seq by Tang et al.); widely adopted 2015–2016
提出者	Saul B. Needleman & Christian D. Wunsch (global); Temple F. Smith & Michael S. Waterman (local)	Azim Surani, Barbara Treutlein, and the Regev/McCarroll groups (foundational droplet-based methods ~2015)
类型	Computational sequence analysis technique	High-throughput single-cell transcriptomic profiling pipeline
开创性文献	Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3), 443–453.	Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33(5), 495–502.
别名	pairwise alignment, multiple sequence alignment, MSA, sequence comparison	scRNA-seq, single-cell transcriptomics, scRNAseq analysis, single-cell gene expression profiling
相关	6	5
摘要	Sequence alignment is a foundational bioinformatics technique that arranges two or more DNA, RNA, or protein sequences to reveal regions of similarity, infer evolutionary relationships, identify functional domains, and map sequencing reads to reference genomes. It underpins virtually every downstream genomic analysis, from variant calling and gene expression quantification to phylogenetics and structural annotation.	Single-cell RNA sequencing (scRNA-seq) analysis characterises gene expression at the resolution of individual cells, enabling discovery of cell types, states, and transitions that are invisible in bulk transcriptomics. Starting from raw sequencing reads, the workflow produces a cell-by-gene count matrix and proceeds through quality control, normalisation, dimensionality reduction, unsupervised clustering, cell-type annotation, and a range of downstream analyses such as trajectory inference and differential expression between cell populations.