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| RaacLogo: a new sequence logo generator by using reduced amino acid clusters | |
| Zheng, Lei; Liu, Dongyang2; Yang, Wuritu; Yang, Lei1; Zuo, Yongchun | |
| 2021 | |
| 发表期刊 | BRIEFINGS IN BIOINFORMATICS
 |
| ISSN | 1467-5463 |
| 卷号 | 22期号:3 |
| 摘要 | Sequence logos give a fast and concise display in visualizing consensus sequence. Protein exhibits greater complexity and diversity than DNA, which usually affects the graphical representation of the logo. Reduced amino acids perform powerful ability for simplifying complexity of sequence alignment, which motivated us to establish RaacLogo. As a new sequence logo generator by using reduced amino acid alphabets, RaacLogo can easily generate many different simplified logos tailored to users by selecting various reduced amino acid alphabets that consisted of more than 40 clustering algorithms. This current web server provides 74 types of reduced amino acid alphabet, which were manually extracted to generate 673 reduced amino acid clusters (RAAC5) for dealing with protein alignment. A two-dimensional selector was proposed for easily selecting desired RAAC5 with underlying biology knowledge. It is anticipated that the RaacLogo web server will play more high-potential roles for protein sequence alignment, topological estimation and protein design experiments. RaacLogo is freely available at http://bioinfor.imu.edu.cn/raaclogo. |
| 关键词 | sequence logo reduced amino acid alphabets protein design web server |
| 学科领域 | Biochemical Research Methods ; Mathematical & Computational Biology |
| DOI | 10.1093/bib/bbaa096 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS关键词 | PROTEINS ; ALPHABET |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000709461300045 |
| 出版者 | OXFORD UNIV PRESS |
| 文献子类 | Article |
| 出版地 | OXFORD |
| EISSN | 1477-4054 |
| 资助机构 | National Natural Science Foundation of China [61702290, 61861036] ; Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region [NJYT-18-B01] ; Fund for Excellent Young Scholars of Inner Mongolia [2017JQ04] |
| 作者邮箱 | leiyang@hrbmu.edu.cn ; yczuo@imu.edu.cn |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/26529 |
| 专题 | 中科院光生物学重点实验室 |
| 作者单位 | 1.Inner Mongolia Univ, Coll Life Sci, State Key Lab Reprod Regulat & Breeding Grassland, Hohhot 010070, Peoples R China 2.Harbin Med Univ, Coll Bioinformat Sci & Technol, Harbin 150081, Peoples R China 3.Chinese Acad Sci, Inst Bot, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zheng, Lei,Liu, Dongyang,Yang, Wuritu,et al. RaacLogo: a new sequence logo generator by using reduced amino acid clusters[J]. BRIEFINGS IN BIOINFORMATICS,2021,22(3). |
| APA | Zheng, Lei,Liu, Dongyang,Yang, Wuritu,Yang, Lei,&Zuo, Yongchun.(2021).RaacLogo: a new sequence logo generator by using reduced amino acid clusters.BRIEFINGS IN BIOINFORMATICS,22(3). |
| MLA | Zheng, Lei,et al."RaacLogo: a new sequence logo generator by using reduced amino acid clusters".BRIEFINGS IN BIOINFORMATICS 22.3(2021). |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Zheng-2021-RaacLogo_（930KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
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