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	デノボトランスクリプトームアセンブリ	HMMER プロファイル検索
分野	バイオインフォマティクス	バイオインフォマティクス
系統	Process / pipeline	Process / pipeline
提唱年	2011	1994
提唱者	Aviv Regev	Sean Eddy
種類	Sequence assembly pipeline	Probabilistic sequence search pipeline
原典	Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., ... & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644-652.	Krogh, A., Brown, M., Mian, I. S., Sjölander, K., & Haussler, D. (1994). Hidden Markov models in computational biology: applications to protein modeling. Journal of Molecular Biology, 235(5), 1501-1531.
別名	transcriptome assembly, de novo assembly, RNA-Seq assembly	profile-hidden Markov model, HMM profile search, HMMER
関連	3	3
概要	De novo transcriptome assembly reconstructs full-length messenger RNA sequences directly from sequencing reads without requiring a reference genome. Pioneered by Regev, Haas, and colleagues, this pipeline enables transcript discovery in non-model organisms and detection of novel isoforms, fusion genes, and splice variants.	HMMER profile search identifies distant protein sequence homologs using probabilistic models of protein families, known as profile Hidden Markov Models (HMMs). Developed by Eddy and colleagues, this method captures sequence variation patterns within protein families and detects homologs with far greater sensitivity than position-weight matrices or pairwise alignment.