期刊
GENETICS AND MOLECULAR RESEARCH
卷 14, 期 4, 页码 17555-17566出版社
FUNPEC-EDITORA
DOI: 10.4238/2015.December.21.28
关键词
Protein function prediction; Comparison; Resources for protein function prediction; Sequence characterization
资金
- CAPES - Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior
- CNPq - Conselho Nacional de Desenvolvimento Cientifico e Tecnologico
- INCT - Institutos Nacionais de Ciencia e Tecnologia da Fixacao Biologica de Nitrogenio
Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据