ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts
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DOI：
10.1186/1471-2105-9-145
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发表时间：
2008-03-06
影响因子：
3
通讯作者：
Kim, Sun
中科院分区：
文献类型：
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作者：
Choi, Kwangmin;Kim, Sun
背景：一旦一个新的基因组被测序，其中一个重要的问题是确定是否存在生物学途径。分析基因组中的生物途径是一项复杂的任务，因为许多生物实体参与途径，并且不同生物体中的生物途径并不相同。因此，计算途径识别和分析涉及许多计算工具和数据库，并且通常与其他生物体中的途径进行比较。这种计算需求远远超出了生物学家的能力，因此非常需要用于重建，注释和分析生物途径的信息系统。我们介绍了一个新的比较途径分析工作台，ComPath，它集成了各种资源和计算工具，使用一个交互式的电子表格风格的Web界面，可靠的pathways analysis.Results：ComPath允许用户比较生物途径在多个基因组使用电子表格风格的Web界面，其中各种基于序列的分析可以进行比较酶（例如，G.序列聚类）和途径（e. G.途径孔识别），搜索基因组以从头预测酶，或与选择的参考基因组相比注释基因组。为了填补途径漏洞或从头进行酶预测，ComPath中集成了多种计算方法，如FASTA，Whole-HMM，CSR-HMM（本文介绍的一种方法）和PDB-域搜索。我们的实验表明，FASTA和CSR-HMM搜索方法在灵敏度方面通常优于Whole-HMM和PDB域搜索方法，但FASTA搜索在特异性方面表现不佳，随着E值截止值的增加，检测到更多的假阳性。总体而言，CSR-HMM搜索方法在灵敏度和特异性方面表现最好。基因邻域和通路邻域（全局网络）可视化工具可用于获得背景信息，这是对传统KEGG图representation.Conclusion的补充：ComPath是一个用于通路重建、注释和分析的交互式工作台，专家可以使用直观和交互式电子表格风格的界面进行各种序列、域和背景分析。
Background: Once a new genome is sequenced, one of the important questions is to determine the presence and absence of biological pathways. Analysis of biological pathways in a genome is a complicated task since a number of biological entities are involved in pathways and biological pathways in different organisms are not identical. Computational pathway identification and analysis thus involves a number of computational tools and databases and typically done in comparison with pathways in other organisms. This computational requirement is much beyond the capability of biologists, so information systems for reconstructing, annotating, and analyzing biological pathways are much needed. We introduce a new comparative pathway analysis workbench, ComPath, which integrates various resources and computational tools using an interactive spreadsheet-style web interface for reliable pathway analyses.Results: ComPath allows users to compare biological pathways in multiple genomes using a spreadsheet style web interface where various sequence-based analysis can be performed either to compare enzymes (e. g. sequence clustering) and pathways (e. g. pathway hole identification), to search a genome for de novo prediction of enzymes, or to annotate a genome in comparison with reference genomes of choice. To fill in pathway holes or make de novo enzyme predictions, multiple computational methods such as FASTA, Whole-HMM, CSR-HMM (a method of our own introduced in this paper), and PDB-domain search are integrated in ComPath. Our experiments show that FASTA and CSR-HMM search methods generally outperform Whole-HMM and PDB-domain search methods in terms of sensitivity, but FASTA search performs poorly in terms of specificity, detecting more false positive as E-value cutoff increases. Overall, CSR-HMM search method performs best in terms of both sensitivity and specificity. Gene neighborhood and pathway neighborhood (global network) visualization tools can be used to get context information that is complementary to conventional KEGG map representation.Conclusion: ComPath is an interactive workbench for pathway reconstruction, annotation, and analysis where experts can perform various sequence, domain, context analysis, using an intuitive and interactive spreadsheet-style interface.