SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci
SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci
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DOI：
10.1093/bib/bbx005
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发表时间：
2018-07-01
影响因子：
9.5
通讯作者：
Chen, Runsheng
中科院分区：
文献类型：
--
作者：
Hao, Yajing;Zhang, Lili;Chen, Runsheng
小蛋白是指长度小于100个氨基酸的蛋白质的总称。近年来，小分子蛋白的鉴定和功能研究进展迅速，一些研究表明，小分子蛋白在发育、肌肉收缩和DNA修复等多种功能中发挥重要作用。识别和表征以前未被识别的小蛋白质可能有助于细胞生物学和人类健康的重要途径。当前的数据库通常有些缺陷，因为它们要么没有系统地收集小蛋白质，要么只包含有限数量的组织和物种中小蛋白质的预测。在这里，我们提出了一个专门设计的网络访问数据库，小蛋白质数据库（SmProt，http：//bioinfo.ibp.ac.cn/SmProt），这是一个记录小蛋白质的数据库。目前发布的SmProt纳入了255 010小蛋白计算或实验确定在291细胞系/组织来自8个流行的物种。该数据库提供包括基本信息（序列、位置、基因名称、生物体等）在内的各种数据。以及具体信息（实验、功能、疾病类型等）。为了便于数据提取，SmProt支持多种搜索选项，包括物种、基因组位置、基因名称及其别名、细胞系/组织、ORF类型、基因类型、PubMed ID和SmProt ID。SmProt还集成了BLAST比对搜索服务，并提供本地UCSC基因组浏览器。此外，SmProt定义了一组高置信度的小蛋白，并预测了小蛋白的功能。
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 search and provides a local UCSC Genome Browser. Additionally, SmProt defines a high-confidence set of small proteins and predicts the functions of the small proteins.