SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci

作者：Yajing Hao, Lili Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Qin Yan, Fuquan Yang, Runsheng Chen · 发表于：Briefings in Bioinformatics · 年份：2017 · DOI：10.1093/bib/bbx005 · 被引用次数：140 · 研究领域：Machine Learning in Bioinformatics、Genomics and Phylogenetic Studies、RNA and protein synthesis mechanisms

Small proteins is the general term for proteins with length shorter than 100 amino acids. Identification and functional studies of small proteins have advanced rapidly in recent years, and several studies have shown that small proteins play important roles in diverse functions including development, muscle contraction and DNA repair. Identification and characterization of previously unrecognized small proteins may contribute in important ways to cell biology and human health. Current databases are generally somewhat deficient in that they have either not collected small proteins systematically, or contain only predictions of small proteins in a limited number of tissues and species. Here, we present a specifically designed web-accessible database, small proteins database (SmProt, http://bioinfo.ibp.ac.cn/SmProt), which is a database documenting small proteins. The current release of SmProt incorporates 255 010 small proteins computationally or experimentally identified in 291 cell lines/tissues derived from eight popular species. The database provides a variety of data including basic information (sequence, location, gene name, organism, etc.) as well as specific information (experiment, function, disease type, etc.). To facilitate data extraction, SmProt supports multiple search options, including species, genome location, gene name and their aliases, cell lines/tissues, ORF type, gene type, PubMed ID and SmProt ID. SmProt also incorporates a service for the BLAST alignment ...