SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. (29th January 2017)

• Record Type: Journal Article
• Authors: Hao, Yajing; Zhang, Lili; Niu, Yiwei; Cai, Tanxi; Luo, Jianjun; He, Shunmin; Zhang, Bao; Zhang, Dejiu; Qin, Yan; Yang, Fuquan; Chen, Runsheng
• Is Part Of: Briefings in bioinformatics. Volume 19:Number 4(2018:Jul.)
• Page Start: 636
• Page End: 643
• Publication Date: 2017-01-29
• Subjects: small proteins -- ribosome profiling -- non-coding RNA -- sORFs; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbx005
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: 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.