综述 2022-IEEE-TCBB：alignment free sequence comparison

Bohnsack, Katrin Sophie, et al. "Alignment-free sequence comparison: A systematic survey from a machine learning perspective." IEEE/ACM Transactions on Computational Biology and Bioinformatics 20.1 (2022): 119-135. https://ieeexplore.ieee.org/abstract/document/9672674

• 被引次数：10；
• 期刊：影响因子 3.702；JCR Q1；中科院大类（工程技术）3区，小类（数学跨学科应用、计算机：跨学科应用）3区
• 核心内容：序列映射到特征空间并在特征空间中进行比较：序列 --> 数值编码、特征生成 --> 问题特异性度量衡量相似性

• 作者信息：

• 标记蓝色说明是近5年发表在比较好的期刊上的论文

开篇：AF方法可用于：

alignment-free method出现：

[16] G. Kucherov, “Evolution of biosequence search algorithms: A brief survey,” Bioinformatics, vol. 35, no. 19, pp. 3547–3552, Oct. 2019.

AF方法推断系统发育：

[17] B. Haubold, “Alignment-free phylogenetics and population genetics,” Briefings Bioinf., vol. 15, no. 3, pp. 407–418, May 2014.

[18] C. X. Chan, G. Bernard, O. Poirion, J. M. Hogan, and M. A. Ragan, “Inferring phylogenies of evolving sequences without multiple sequence alignment,” Sci. Rep., vol. 4, no. 1, May 2015, Art. no. 6504.

[19] K. Hatje and M. Kollmar, “A phylogenetic analysis of the brassi- cales clade based on an alignment-free sequence comparison method,” Front. Plant Sci., vol. 3, 2012, Art. no. 192.

AF方法用于元基因组：

[20] Y.-W. Wu and Y. Ye, “A novel abundance-based algorithm for binning metagenomic sequences using l-tuples,” J. Comput. Biol.: A J. Comput. Mol. Cell Biol., vol. 18, no. 3, pp. 523–534, Mar. 2011.

[21] G. Leung and M. B. Eisen, “Identifying Cis-regulatory sequences by word profile similarity,” PLoS One, vol. 4, no. 9, Sep. 2009, Art. no. e6901.

AF方法用于数据库搜索：

[22] B. T. et al., “RAFTS3G: An efficient and versatile clustering soft- ware to analyses in large protein datasets,” BMC Bioinf., vol. 20, no. 1, Jul. 2019, Art. no. 392.

AF方法用于N