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| Bayesian Sequence Alignment× | RNA-seq diferencijalna ekspresija× | |
|---|---|---|
| Područje | Bioinformatika | Bioinformatika |
| Obitelj | Process / pipeline | Process / pipeline |
| Godina nastanka≠ | 2001–2005 | 2008–2010 (RNA-seq DE methodology established) |
| Tvorac≠ | Ian Holmes & William J. Bruno; Benjamin Redelings & Marc Suchard | Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010) |
| Vrsta≠ | Probabilistic computational method | Quantitative genomics pipeline |
| Temeljni izvor≠ | Redelings, B. D., & Suchard, M. A. (2005). Joint Bayesian estimation of alignment and phylogeny. Systematic Biology, 54(3), 401–418. link ↗ | Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. DOI ↗ |
| Drugi nazivi | Bayesian MSA, probabilistic sequence alignment, statistical alignment, BAli-Phy alignment | RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA |
| Srodne≠ | 5 | 6 |
| Sažetak≠ | Bayesian sequence alignment treats the alignment of biological sequences (DNA, RNA, or protein) as a probabilistic inference problem rather than a deterministic optimization. Instead of returning a single best alignment, it samples from a posterior distribution over all plausible alignments given a substitution model and gap penalty priors, thereby quantifying alignment uncertainty. It is particularly valuable when downstream analyses such as phylogenetic inference or functional annotation are sensitive to alignment error. | RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values. |
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