Rodriguez Alexis A, Bompada Tanuja, Syed Mustafa, Shah Parantu K, Maltsev Natalia
Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439, USA.
Bioinformatics. 2007 Nov 15;23(22):2961-8. doi: 10.1093/bioinformatics/btm421. Epub 2007 Sep 13.
Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.
Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, 'binning' of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.
可获得大量分类学和表型多样的生物体的基因组和酶数据，这使得探索导致酶功能多样化的适应性机制成为可能。我们展示了Chisel，这是一个用于对酶的进化变异进行自动、高分辨率分析的计算框架和流程。Chisel允许自动以及交互式地识别和表征酶序列。这些知识可用于比较基因组学、微生物诊断、代谢工程、药物设计和宏基因组分析。
Chisel是一个综合资源，包含8575个聚类以及针对939种不同酶功能的后续计算模型，并且在数据充足时还包含它们的分类学变异。展示了Chisel在新测序基因组中酶序列识别、特定生物体代谢网络分析、宏基因组“分箱”及其他生物学问题中的应用。我们还对Chisel与其他类似资源的性能以及希瓦氏菌MR1基因组上的手动注释进行了全面分析。
