{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:24:00Z","timestamp":1778642640689,"version":"3.51.4"},"reference-count":162,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,12,5]],"date-time":"2019-12-05T00:00:00Z","timestamp":1575504000000},"content-version":"vor","delay-in-days":338,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Nature Scientific Foundation of China","doi-asserted-by":"crossref","award":["61561036"],"award-info":[{"award-number":["61561036"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Scientific Foundation of China","doi-asserted-by":"crossref","award":["61702290"],"award-info":[{"award-number":["61702290"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region","award":["NJYT-18-B01"],"award-info":[{"award-number":["NJYT-18-B01"]}]},{"name":"Fund for Excellent Young Scholars of Inner Mongolia","award":["2017JQ04"],"award-info":[{"award-number":["2017JQ04"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>By reducing amino acid alphabet, the protein complexity can be significantly simplified, which could improve computational efficiency, decrease information redundancy and reduce chance of overfitting. Although some reduced alphabets have been proposed, different classification rules could produce distinctive results for protein sequence analysis. Thus, it is urgent to construct a systematical frame for reduced alphabets. In this work, we constructed a comprehensive web server called RAACBook for protein sequence analysis and machine learning application by integrating reduction alphabets. The web server contains three parts: (i) 74 types of reduced amino acid alphabet were manually extracted to generate 673 reduced amino acid clusters (RAACs) for dealing with unique protein problems. It is easy for users to select desired RAACs from a multilayer browser tool. (ii) An online tool was developed to analyze primary sequence of protein. The tool could produce K-tuple reduced amino acid composition by defining three correlation parameters (K-tuple, g-gap, \u03bb-correlation). The results are visualized as sequence alignment, mergence of RAA composition, feature distribution and logo of reduced sequence. (iii) The machine learning server is provided to train the model of protein classification based on K-tuple RAAC. The optimal model could be selected according to the evaluation indexes (ROC, AUC, MCC, etc.). In conclusion, RAACBook presents a powerful and user-friendly service in protein sequence analysis and computational proteomics. RAACBook can be freely available at http:\/\/bioinfor.imu.edu.cn\/raacbook.<\/jats:p><jats:p>Database URL: http:\/\/bioinfor.imu.edu.cn\/raacbook<\/jats:p>","DOI":"10.1093\/database\/baz131","type":"journal-article","created":{"date-parts":[[2019,10,19]],"date-time":"2019-10-19T11:09:05Z","timestamp":1571483345000},"source":"Crossref","is-referenced-by-count":60,"title":["RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou\u2019s five-step rule"],"prefix":"10.1093","volume":"2019","author":[{"given":"Lei","family":"Zheng","sequence":"first","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shenghui","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nengjiang","family":"Mu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoyue","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiayu","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Chang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road No.157, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6065-7835","authenticated-orcid":false,"given":"Yongchun","family":"Zuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, 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