FFPred 3: feature-based function prediction for all Gene Ontology domains.
FFPred 3: feature-based function prediction for all Gene Ontology domains.
复制标题
DOI：
10.1038/srep31865
复制
发表时间：
2016-08-26
影响因子：
4.6
通讯作者：
Jones DT
中科院分区：
文献类型：
--
作者：
Cozzetto D;Minneci F;Currant H;Jones DT
几十年来，预测蛋白质功能一直是生物信息学的一个主要目标，由于最近社区范围内的盲测旨在对基因组规模上的可用工具进行基准测试，它获得了新的动力。基于序列的预测器，特别是那些执行基于同源性的转移的预测器，仍然是最受欢迎的，但对它们的局限性的日益了解刺激了互补方法的发展，这些方法主要利用机器学习。在这里，我们提出了FFPred 3，这是为了分配基因本体论术语的人类蛋白质链，当同源性与特征蛋白质可以提供很少的帮助。预测是通过对一系列支持向量机（SVM）扫描输入序列，每个检查蛋白质功能和生物物理属性之间的关系，描述二级结构，跨膜螺旋，固有的无序区域，信号肽和其他图案。此更新具有更大的SVM库，首次将其覆盖范围扩展到细胞成分子本体，这是由于在功能注释的关键评估中建立了一个专用的评估类别。这种方法的有效性是通过基准测试实验证明，其有用性是通过分析潜在的功能后果的选择性剪接在人类和他们的关系模式的生物特征。
Predicting protein function has been a major goal of bioinformatics for several decades, and it has gained fresh momentum thanks to recent community-wide blind tests aimed at benchmarking available tools on a genomic scale. Sequence-based predictors, especially those performing homology-based transfers, remain the most popular but increasing understanding of their limitations has stimulated the development of complementary approaches, which mostly exploit machine learning. Here we present FFPred 3, which is intended for assigning Gene Ontology terms to human protein chains, when homology with characterized proteins can provide little aid. Predictions are made by scanning the input sequences against an array of Support Vector Machines (SVMs), each examining the relationship between protein function and biophysical attributes describing secondary structure, transmembrane helices, intrinsically disordered regions, signal peptides and other motifs. This update features a larger SVM library that extends its coverage to the cellular component sub-ontology for the first time, prompted by the establishment of a dedicated evaluation category within the Critical Assessment of Functional Annotation. The effectiveness of this approach is demonstrated through benchmarking experiments, and its usefulness is illustrated by analysing the potential functional consequences of alternative splicing in human and their relationship to patterns of biological features.