Software Suite for Gene and Protein Annotation Prediction and Similarity Search
Software Suite for Gene and Protein Annotation Prediction and Similarity Search
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DOI：
10.1109/tcbb.2014.2382127
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发表时间：
2015-07-01
影响因子：
4.5
通讯作者：
Masseroli, Marco
中科院分区：
文献类型：
--
作者：
Chicco, Davide;Masseroli, Marco
在计算生物学领域，机器学习算法是许多应用的关键工具，包括基于现有的生物分子注释来预测基因功能。此外，它们也可用于计算基因或蛋白质之间的相似性。在此，我们描述并讨论我们开发的一个软件套件，该套件实现了一些此类预测方法以及一种基于潜在语义索引（LSI）的计算技术，并将其公开，这种技术利用推断出的和现有的注释来搜索语义相似的基因。该套件由三个组件组成。BioAnnotationPredictor是一个计算软件模块，它基于现有注释的奇异值分解来预测新的基因功能。SimilBio是一个网络模块，它利用BioAnnotationPredictor提供的或预测的注释，通过LSI发现基因之间的相似性。该套件还包括SemSim，这是一个基于这些模块构建的新的网络服务，允许以编程方式访问它们。我们将SemSim集成到生物搜索计算框架（http://www.bioinformatics.deib.polimi.it/bio - seco/seco/）中，用户可以利用搜索计算技术在多个集成的网络服务上运行多主题复杂查询。因此，研究人员可以获得涉及基因之间功能相似性计算的排序答案，以支持生物医学知识发现。
In the computational biology community, machine learning algorithms are key instruments for many applications, including the prediction of gene-functions based upon the available biomolecular annotations. Additionally, they may also be employed to compute similarity between genes or proteins. Here, we describe and discuss a software suite we developed to implement and make publicly available some of such prediction methods and a computational technique based upon Latent Semantic Indexing (LSI), which leverages both inferred and available annotations to search for semantically similar genes. The suite consists of three components. BioAnnotationPredictor is a computational software module to predict new gene-functions based upon Singular Value Decomposition of available annotations. SimilBio is a Web module that leverages annotations available or predicted by BioAnnotationPredictor to discover similarities between genes via LSI. The suite includes also SemSim, a new Web service built upon these modules to allow accessing them programmatically. We integrated SemSim in the Bio Search Computing framework (http://www.bioinformatics.deib.polimi.it/bio-seco/seco/), where users can exploit the Search Computing technology to run multi-topic complex queries on multiple integrated Web services. Accordingly, researchers may obtain ranked answers involving the computation of the functional similarity between genes in support of biomedical knowledge discovery.